From 7c67e87772efeb404455c0675eb5eb3a01ddaab0 Mon Sep 17 00:00:00 2001 From: Florent Leclercq Date: Wed, 26 Oct 2016 17:44:07 +0100 Subject: [PATCH] added borg_sdss_diva --- borg_sdss_diva/README.md | 116 ++++ borg_sdss_diva/borg_sdss_diva.ipynb | 872 ++++++++++++++++++++++++++++ borg_sdss_diva/borg_sdss_diva.py | 26 + 3 files changed, 1014 insertions(+) create mode 100644 borg_sdss_diva/README.md create mode 100644 borg_sdss_diva/borg_sdss_diva.ipynb create mode 100644 borg_sdss_diva/borg_sdss_diva.py diff --git a/borg_sdss_diva/README.md b/borg_sdss_diva/README.md new file mode 100644 index 0000000..553a9eb --- /dev/null +++ b/borg_sdss_diva/README.md @@ -0,0 +1,116 @@ +============================================== +BORG SDSS data products +============================================== + +:Authors: Florent Leclercq, Jens Jasche, Guilhem Lavaux, Benjamin Wandelt +:Last update: 16-06-2016 + +---------------------- +File Contents +---------------------- + +Including this file you should have received a copy of in total three files: + + README.rst + + borg_sdss_diva.npz + + example.py + + +README.rst :This file contains the information you are currently reading. + +borg_sdss_diva.npz :This file contains the maps obtained by Leclercq et al. (2016a), who performed + a Bayesian analysis of the cosmic web in the SDSS volume. The results are four + probabilistic maps of the voids, sheets, filaments, and clusters. + Structures are defined using the DIVA algorithm (Lavaux & Wandelt 2010) + Data is provided in terms of a standard 3D numpy array and can easily be accessed and + processed with the open source Python programming language. For further details on + the data and employed methods please consult the manuscript Leclercq et al. (2016a), + of which the reference is provided below. + +example.py :This file is an example script to be executed with the Python programming language. + The script exemplifies loading and plotting the data contained in borg_sdss_diva.npz. + This script can be used to reproduce figure 3 (top row) in Leclercq et al. (2016a). + +---------------------- +Usage +---------------------- + +The file borg_sdss_diva.npz contains the probabilistic structure types maps in a standard uncompressed .npz format. +To load and process the data with the Python programming language execute the following commands: + + import numpy as np + diva=np.load('borg_sdss_diva.npz') + +To access the 3D structure maps use: + + voids=diva['voids'] + sheets=diva['sheets'] + filaments=diva['filaments'] + clusters=diva['clusters'] + +Individual voxels in this 3D volumetric data cube can be accessed as follows: + + voids_ijk=voids[k,j,i], + +where i,j and k index voxel positions along the x,y and z axes respectively. +All indices run from 0 to 255. + +The ranges describing the extent of the cubic cartesian volume along +the x,y and z axes can be accessed as follows: + + xmin=diva['ranges'][0] + xmax=diva['ranges'][1] + + ymin=diva['ranges'][2] + ymax=diva['ranges'][3] + + zmin=diva['ranges'][4] + zmax=diva['ranges'][5] + +Units are Mpc/h. + +(Note that all the maps that are part of the BORG SDSS data products have consistent consistent +coordinate systems. The coordinate transform to change from Cartesian to spherical coordinates +and vice versa is given in appendix B of Jasche et al. 2015) + +A showcase of loading and plotting this data is provided by the file example.py, +a copy of which you should have received along with this file. + +---------------------- +Credits +---------------------- + +If you are using this data in your publications please cite the +following publication: + + Leclercq, F. and Jasche, J. and Lavaux, G. and Wandelt, B. (2016a) + Inference and classifications of the Lagrangian dark matter sheet in the SDSS + arXiv:1601.00093 [astro-ph.CO] + +As cosmic web analysis is a derived product of the BORG SDSS analysis, we also kindly +ask you to cite the following publications: + + Jasche, J. and Wandelt, B. D. (2013) + Bayesian physical reconstruction of initial conditions from large-scale structure surveys + Monthly Notices of the Royal Astronomical Society 432, 894-913 (2013) + arXiv:1203.3639 [astro-ph.CO] + +and: + + Jasche, J. and Leclercq, F. and Wandelt, B. D. (2015) + Past and present cosmic structure in the SDSS DR7 main sample + Journal of Cosmology and Astroparticle Physics 01, 036 (2015) + arXiv:1409.6308 [astro-ph.CO] + +as well as the 'DIVA' paper: + + Lavaux, G. and Wandelt, B. D. (2010) + Precision cosmology with voids: definition, methods, dynamics + Monthly Notices of the Royal Astronomical Society 403, 1392-1408 (2010) + arXiv:0906.4101 [astro-ph.CO] + +We suggest, for example, the following sentence: +'This work uses the cosmic web maps obtained by Leclercq et al. (2016a), based on the DIVA definition (Lavaux & Wandelt 2010) +and on the analysis of the SDSS (Jasche et al. 2015) by the BORG algorithm (Jasche & Wandelt 2013).' diff --git a/borg_sdss_diva/borg_sdss_diva.ipynb b/borg_sdss_diva/borg_sdss_diva.ipynb new file mode 100644 index 0000000..cf4a574 --- /dev/null +++ b/borg_sdss_diva/borg_sdss_diva.ipynb @@ -0,0 +1,872 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": { + "collapsed": true + }, + "source": [ + "# Import data" + ] + }, + { + "cell_type": "code", + "execution_count": 1, + "metadata": { + "collapsed": false + }, + "outputs": [], + "source": [ + "import numpy as np\n", + "diva = np.load('borg_sdss_diva.npz')\n", + "\n", + "#Minimum and maximum position along the x-axis in Mpc/h\n", + "xmin=diva['ranges'][0]\n", + "xmax=diva['ranges'][1]\n", + "\n", + "#Minimum and maximum position along the y-axis in Mpc/h\n", + "ymin=diva['ranges'][2]\n", + "ymax=diva['ranges'][3]\n", + "\n", + "#Minimum and maximum position along the z-axis in Mpc/h\n", + "zmin=diva['ranges'][4]\n", + "zmax=diva['ranges'][5]\n", + "\n", + "#3D probabilistic maps for DIVA structures\n", + "voids=diva['voids']\n", + "sheets=diva['sheets']\n", + "filaments=diva['filaments']\n", + "clusters=diva['clusters']" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Example plot" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": { + "collapsed": false, + "scrolled": false + }, + "outputs": [ + { + "data": { + "application/javascript": [ + "/* Put everything inside the global mpl namespace */\n", + "window.mpl = {};\n", + "\n", + "mpl.get_websocket_type = function() {\n", + " if (typeof(WebSocket) !== 'undefined') {\n", + " return WebSocket;\n", + " } else if (typeof(MozWebSocket) !== 'undefined') {\n", + " return MozWebSocket;\n", + " } else {\n", + " alert('Your browser does not have WebSocket support.' +\n", + " 'Please try Chrome, Safari or Firefox ≥ 6. 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