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updated examples
This commit is contained in:
P.M. Sutter
parent
ad3e5d1577
commit
4494fcdd2f
2 changed files with 108 additions and 242 deletions
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@ -19,18 +19,10 @@
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#+
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#!/usr/bin/env python
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# does analysis in real space assuming LCDM cosmology
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import os
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import numpy as np
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from void_python_tools.backend.classes import *
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# does full void analysis. Also generates 2d/1d stacked plots and hubble diagram
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# to combine multiple samples:
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# For example, combining dim from 0.0-0.1 and bright from 0.1-0.2:
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# 1) add dim+bright to sampleList - "+" is required to detect combo!
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# if True, will scan log files for last known completed state and run from there
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continueRun = False
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@ -38,213 +30,75 @@ continueRun = False
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# 1 : extract redshift slices from data
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# 2 : void extraction using zobov
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# 3 : removal of small voids and voids near the edge
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# 4 : void stacking and combining
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# 5 : 1-d and 2-d profile generation
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# 6 : fitting and plotting stacked voids
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# 7 : determination of error bars (if requested)
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# 8 : hubble diagram generation
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# 9 : liklihood determination
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startCatalogStage = 1
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endCatalogStage = 1
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endCatalogStage = 3
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catalogName = "lcdm"
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# a global name to give
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#catalogName = "lcdm"
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# where main data files are present/will go
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workDir = os.getenv("HOME")+"/workspace/Voids/sdss_dr7LCDM/"
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# directory for input data files
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inputDataDir = os.getenv("HOME")+"/workspace/Voids/catalogs/nyuvagc/"
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# void catalog output directory
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workDir = os.getenv("HOME")+"/workspace/Voids/sdss_dr7LCDM/"
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# output directory for log files
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logDir = os.getenv("PWD")+"/../logs/sdss_dr7LCDM"
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# output directory for figures
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figDir = os.getenv("PWD")+"/../figs/sdss_dr7LCDM"
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# you need to set these manually: point to ZOBOV and C_TOOLS in VIDE directory
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ZOBOV_PATH = os.getenv("PWD")+"/../zobov/"
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CTOOLS_PATH = os.getenv("PWD")+"/../c_tools/"
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freshStack = True # "no" to continue building onto existing stacked voids
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# if true, convert to comoving space using LCDM cosmology
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useComoving = True
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errorBars = "CALCULATED" # "ESTIMATED" for error bars from multiple null tests
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#errorBars = "ESTIMATED" # "ESTIMATED" for error bars from multiple null tests
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# "CALCULATED" to use fitting procedure
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numIncoherentRuns = 100
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ranSeed = 101010
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useComoving = True # if true, convert to real space using LCDM cosmology
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# try different portions of data. available options: "all, central, edge"
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dataPortions = ["central", "all"]
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numZobovDivisions = 2
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# optimization: maximum number of parallel threads to use
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numZobovThreads = 2
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# optimization: number of subdivisions of the box
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numZobovDivisions = 2
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# don't change this
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dataSampleList = []
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# define your volume-limited samples
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newSample = Sample(
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# path to galaxy file is inputDataDir+dataFile
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dataFile = "filename.dat"
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newSample = Sample(fullName = "lss.dr72dim1.dat",
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# full name for this sample
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fullName = "lss.dr72dim1.dat",
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# a convenient nickname
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nickName = "dim1",
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# don't change this
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dataType = "observation",
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# HEALpix mask file
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maskFile = inputDataDir+"/healpix/rast_window_512.fits",
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selFunFile = inputDataDir+"/czselfunc.all.dr72dim1.dat",
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# max and min redshifts of galaxies in your sample
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zBoundary = (0.0, 0.05),
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# max and min redshifts where you want to find voids
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zRange = (0.0, 0.05),
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# TODO
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skyFraction = 0.19,
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minVoidRadius = 3.479,
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fakeDensity = 0.01,
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volumeLimited = True,
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includeInHubble = False,
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partOfCombo = True,
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isCombo = False,
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comboList= None)
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newSample.addStack(0.0, 0.1, 8, 12, False, True)
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newSample.addStack(0.0, 0.1, 12, 16, False, True)
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newSample.addStack(0.0, 0.1, 16, 20, False, True)
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newSample.addStack(0.0, 0.1, 20, 28, False, True)
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dataSampleList.append(newSample)
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newSample = Sample(fullName = "lss.dr72dim2.dat",
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nickName = "dim2",
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dataType = "observation",
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maskFile = inputDataDir+"/healpix/rast_window_512.fits",
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selFunFile = inputDataDir+"/czselfunc.all.dr72dim2.dat",
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zBoundary = (0.0, 0.1),
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zRange = (0.05, 0.1),
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skyFraction = 0.19,
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minVoidRadius = 4.723,
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fakeDensity = 0.01,
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volumeLimited = True,
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includeInHubble = False,
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partOfCombo = True,
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isCombo = False,
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comboList= None)
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newSample.addStack(0.0, 0.1, 8, 12, False, True)
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newSample.addStack(0.0, 0.1, 12, 16, False, True)
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newSample.addStack(0.0, 0.1, 16, 20, False, True)
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newSample.addStack(0.0, 0.1, 20, 28, False, True)
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dataSampleList.append(newSample)
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newSample = Sample(fullName = "lss.dr72dim1+dim2.dat",
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nickName = "dim1+dim2",
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dataType = "observation",
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maskFile = inputDataDir+"/healpix/rast_window_512.fits",
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selFunFile = inputDataDir+"/czselfunc.all.dr72dim.dat",
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zBoundary = (0.0, 0.1),
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zRange = (0.0, 0.1),
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skyFraction = 0.19,
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minVoidRadius = 4.723,
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fakeDensity = 0.01,
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profileBinSize = "auto",
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volumeLimited = True,
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includeInHubble = True,
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partOfCombo = False,
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isCombo = True,
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comboList= ("lss.dr72dim1.dat", "lss.dr72dim2.dat"))
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newSample.addStack(0.0, 0.1, 8, 12, True, False)
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newSample.addStack(0.0, 0.1, 12, 16, True, False)
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newSample.addStack(0.0, 0.1, 16, 20, True, False)
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newSample.addStack(0.0, 0.1, 20, 28, True, False)
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dataSampleList.append(newSample)
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newSample = Sample(fullName = "lss.dr72bright1.dat",
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nickName = "bright1",
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dataType = "observation",
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maskFile = inputDataDir+"/healpix/rast_window_512.fits",
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selFunFile = inputDataDir+"/czselfunc.all.dr72bright1.dat",
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zBoundary = (0.0, 0.15),
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zRange = (0.1, 0.15),
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skyFraction = 0.19,
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minVoidRadius = 6.763,
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fakeDensity = 0.01,
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volumeLimited = True,
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includeInHubble = False,
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partOfCombo = True,
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isCombo = False,
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comboList= None)
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newSample.addStack(0.1, 0.2, 13, 20, False, True)
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newSample.addStack(0.1, 0.2, 20, 28, False, True)
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newSample.addStack(0.1, 0.2, 28, 36, False, True)
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newSample.addStack(0.1, 0.2, 36, 44, False, True)
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dataSampleList.append(newSample)
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newSample = Sample(fullName = "lss.dr72bright2.dat",
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nickName = "bright2",
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dataType = "observation",
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maskFile = inputDataDir+"/healpix/rast_window_512.fits",
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selFunFile = inputDataDir+"/czselfunc.all.dr72bright2.dat",
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zBoundary = (0.0, 0.2),
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zRange = (0.15, 0.2),
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skyFraction = 0.19,
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minVoidRadius = 10.844,
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fakeDensity = 0.001,
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volumeLimited = True,
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includeInHubble = False,
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partOfCombo = True,
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isCombo = False,
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comboList= None)
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newSample.addStack(0.1, 0.2, 13, 20, False, True)
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newSample.addStack(0.1, 0.2, 20, 28, False, True)
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newSample.addStack(0.1, 0.2, 28, 36, False, True)
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newSample.addStack(0.1, 0.2, 36, 44, False, True)
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dataSampleList.append(newSample)
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newSample = Sample(fullName = "lss.dr72bright1+bright2.dat",
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nickName = "bright1+bright2",
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dataType = "observation",
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maskFile = inputDataDir+"/healpix/rast_window_512.fits",
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zBoundary = (0.0, 0.2),
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zRange = (0.1, 0.2),
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skyFraction = 0.19,
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# leave this at -1 for mean particle separation, or
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# specify your own in Mpc/h
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minVoidRadius = -1,
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fakeDensity = -1,
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profileBinSize = "auto",
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volumeLimited = True,
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includeInHubble = True,
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partOfCombo = False,
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isCombo = True,
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comboList= ("lss.dr72bright1.dat", "lss.dr72bright2.dat"))
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newSample.addStack(0.1, 0.2, 13, 20, True, False)
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newSample.addStack(0.1, 0.2, 20, 28, True, False)
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newSample.addStack(0.1, 0.2, 28, 36, True, False)
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newSample.addStack(0.1, 0.2, 36, 44, True, False)
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# density of mock particles in cubic Mpc/h
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fakeDensity = 0.01,
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)
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dataSampleList.append(newSample)
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newSample = Sample(fullName = "lss.dr72lrgdim.dat",
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nickName = "lrgdim",
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dataType = "observation",
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maskFile = inputDataDir+"/healpix/rast_window_512.fits",
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selFunFile = inputDataDir+"/czselfunc.all.dr72lrgdim.dat",
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zBoundary = (0.16, 0.36),
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zRange = (0.16, 0.36),
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skyFraction = 0.19,
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minVoidRadius = 24,
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fakeDensity = 0.001,
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profileBinSize = 2, # KEEP
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volumeLimited = True,
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includeInHubble = True,
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partOfCombo = False,
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isCombo = False,
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comboList= None)
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newSample.addStack(0.16, 0.36, 54, 70, True, False, zMinPlot=0.2)
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newSample.addStack(0.16, 0.36, 70, 106, True, False, zMinPlot=0.2)
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dataSampleList.append(newSample)
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newSample = Sample(fullName = "lss.dr72lrgbright.dat",
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nickName = "lrgbright",
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dataType = "observation",
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maskFile = inputDataDir+"/healpix/rast_window_512.fits",
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selFunFile = inputDataDir+"/czselfunc.all.dr72lrgbright.dat",
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zBoundary = (0.36, 0.44),
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zRange = (0.36, 0.44),
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skyFraction = 0.19,
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minVoidRadius = 38,
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fakeDensity = 0.001,
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profileBinSize = "auto",
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volumeLimited = True,
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includeInHubble = False,
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partOfCombo = False,
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isCombo = False,
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comboList= None)
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newSample.addStack(0.36, 0.44, 76, 92, False, False)
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newSample.addStack(0.36, 0.44, 92, 108, False, False)
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dataSampleList.append(newSample)
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# repeat the above block for any other samples
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