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P.M. Sutter 2014-04-21 23:58:17 -04:00
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pipeline/datasets/example_observation.py Normal file
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#+
# VIDE -- Void IDentification and Examination -- ./pipeline/sdss/sdss_dr7LCDM.py
# Copyright (C) 2010-2013 Guilhem Lavaux
# Copyright (C) 2011-2013 P. M. Sutter
#
# 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; version 2 of the License.
#
#
# 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.
#+
#!/usr/bin/env python
# does analysis in real space assuming LCDM cosmology
import os
import numpy as np
from void_python_tools.backend.classes import *
# does full void analysis. Also generates 2d/1d stacked plots and hubble diagram
# to combine multiple samples:
# For example, combining dim from 0.0-0.1 and bright from 0.1-0.2:
# 1) add dim+bright to sampleList - "+" is required to detect combo!
# if True, will scan log files for last known completed state and run from there
continueRun = False
# stages:
# 1 : extract redshift slices from data
# 2 : void extraction using zobov
# 3 : removal of small voids and voids near the edge
# 4 : void stacking and combining
# 5 : 1-d and 2-d profile generation
# 6 : fitting and plotting stacked voids
# 7 : determination of error bars (if requested)
# 8 : hubble diagram generation
# 9 : liklihood determination
startCatalogStage = 1
endCatalogStage = 1
catalogName = "lcdm"
# where main data files are present/will go
workDir = os.getenv("HOME")+"/workspace/Voids/sdss_dr7LCDM/"
inputDataDir = os.getenv("HOME")+"/workspace/Voids/catalogs/nyuvagc/"
logDir = os.getenv("PWD")+"/../logs/sdss_dr7LCDM"
figDir = os.getenv("PWD")+"/../figs/sdss_dr7LCDM"
ZOBOV_PATH = os.getenv("PWD")+"/../zobov/"
CTOOLS_PATH = os.getenv("PWD")+"/../c_tools/"
freshStack = True # "no" to continue building onto existing stacked voids
errorBars = "CALCULATED" # "ESTIMATED" for error bars from multiple null tests
#errorBars = "ESTIMATED" # "ESTIMATED" for error bars from multiple null tests
# "CALCULATED" to use fitting procedure
numIncoherentRuns = 100
ranSeed = 101010
useComoving = True # if true, convert to real space using LCDM cosmology
# try different portions of data. available options: "all, central, edge"
dataPortions = ["central", "all"]
numZobovDivisions = 2
numZobovThreads = 2
dataSampleList = []
newSample = Sample(fullName = "lss.dr72dim1.dat",
nickName = "dim1",
dataType = "observation",
maskFile = inputDataDir+"/healpix/rast_window_512.fits",
selFunFile = inputDataDir+"/czselfunc.all.dr72dim1.dat",
zBoundary = (0.0, 0.05),
zRange = (0.0, 0.05),
skyFraction = 0.19,
minVoidRadius = 3.479,
fakeDensity = 0.01,
volumeLimited = True,
includeInHubble = False,
partOfCombo = True,
isCombo = False,
comboList= None)
newSample.addStack(0.0, 0.1, 8, 12, False, True)
newSample.addStack(0.0, 0.1, 12, 16, False, True)
newSample.addStack(0.0, 0.1, 16, 20, False, True)
newSample.addStack(0.0, 0.1, 20, 28, False, True)
dataSampleList.append(newSample)
newSample = Sample(fullName = "lss.dr72dim2.dat",
nickName = "dim2",
dataType = "observation",
maskFile = inputDataDir+"/healpix/rast_window_512.fits",
selFunFile = inputDataDir+"/czselfunc.all.dr72dim2.dat",
zBoundary = (0.0, 0.1),
zRange = (0.05, 0.1),
skyFraction = 0.19,
minVoidRadius = 4.723,
fakeDensity = 0.01,
volumeLimited = True,
includeInHubble = False,
partOfCombo = True,
isCombo = False,
comboList= None)
newSample.addStack(0.0, 0.1, 8, 12, False, True)
newSample.addStack(0.0, 0.1, 12, 16, False, True)
newSample.addStack(0.0, 0.1, 16, 20, False, True)
newSample.addStack(0.0, 0.1, 20, 28, False, True)
dataSampleList.append(newSample)
newSample = Sample(fullName = "lss.dr72dim1+dim2.dat",
nickName = "dim1+dim2",
dataType = "observation",
maskFile = inputDataDir+"/healpix/rast_window_512.fits",
selFunFile = inputDataDir+"/czselfunc.all.dr72dim.dat",
zBoundary = (0.0, 0.1),
zRange = (0.0, 0.1),
skyFraction = 0.19,
minVoidRadius = 4.723,
fakeDensity = 0.01,
profileBinSize = "auto",
volumeLimited = True,
includeInHubble = True,
partOfCombo = False,
isCombo = True,
comboList= ("lss.dr72dim1.dat", "lss.dr72dim2.dat"))
newSample.addStack(0.0, 0.1, 8, 12, True, False)
newSample.addStack(0.0, 0.1, 12, 16, True, False)
newSample.addStack(0.0, 0.1, 16, 20, True, False)
newSample.addStack(0.0, 0.1, 20, 28, True, False)
dataSampleList.append(newSample)
newSample = Sample(fullName = "lss.dr72bright1.dat",
nickName = "bright1",
dataType = "observation",
maskFile = inputDataDir+"/healpix/rast_window_512.fits",
selFunFile = inputDataDir+"/czselfunc.all.dr72bright1.dat",
zBoundary = (0.0, 0.15),
zRange = (0.1, 0.15),
skyFraction = 0.19,
minVoidRadius = 6.763,
fakeDensity = 0.01,
volumeLimited = True,
includeInHubble = False,
partOfCombo = True,
isCombo = False,
comboList= None)
newSample.addStack(0.1, 0.2, 13, 20, False, True)
newSample.addStack(0.1, 0.2, 20, 28, False, True)
newSample.addStack(0.1, 0.2, 28, 36, False, True)
newSample.addStack(0.1, 0.2, 36, 44, False, True)
dataSampleList.append(newSample)
newSample = Sample(fullName = "lss.dr72bright2.dat",
nickName = "bright2",
dataType = "observation",
maskFile = inputDataDir+"/healpix/rast_window_512.fits",
selFunFile = inputDataDir+"/czselfunc.all.dr72bright2.dat",
zBoundary = (0.0, 0.2),
zRange = (0.15, 0.2),
skyFraction = 0.19,
minVoidRadius = 10.844,
fakeDensity = 0.001,
volumeLimited = True,
includeInHubble = False,
partOfCombo = True,
isCombo = False,
comboList= None)
newSample.addStack(0.1, 0.2, 13, 20, False, True)
newSample.addStack(0.1, 0.2, 20, 28, False, True)
newSample.addStack(0.1, 0.2, 28, 36, False, True)
newSample.addStack(0.1, 0.2, 36, 44, False, True)
dataSampleList.append(newSample)
newSample = Sample(fullName = "lss.dr72bright1+bright2.dat",
nickName = "bright1+bright2",
dataType = "observation",
maskFile = inputDataDir+"/healpix/rast_window_512.fits",
zBoundary = (0.0, 0.2),
zRange = (0.1, 0.2),
skyFraction = 0.19,
minVoidRadius = -1,
fakeDensity = -1,
profileBinSize = "auto",
volumeLimited = True,
includeInHubble = True,
partOfCombo = False,
isCombo = True,
comboList= ("lss.dr72bright1.dat", "lss.dr72bright2.dat"))
newSample.addStack(0.1, 0.2, 13, 20, True, False)
newSample.addStack(0.1, 0.2, 20, 28, True, False)
newSample.addStack(0.1, 0.2, 28, 36, True, False)
newSample.addStack(0.1, 0.2, 36, 44, True, False)
dataSampleList.append(newSample)
newSample = Sample(fullName = "lss.dr72lrgdim.dat",
nickName = "lrgdim",
dataType = "observation",
maskFile = inputDataDir+"/healpix/rast_window_512.fits",
selFunFile = inputDataDir+"/czselfunc.all.dr72lrgdim.dat",
zBoundary = (0.16, 0.36),
zRange = (0.16, 0.36),
skyFraction = 0.19,
minVoidRadius = 24,
fakeDensity = 0.001,
profileBinSize = 2, # KEEP
volumeLimited = True,
includeInHubble = True,
partOfCombo = False,
isCombo = False,
comboList= None)
newSample.addStack(0.16, 0.36, 54, 70, True, False, zMinPlot=0.2)
newSample.addStack(0.16, 0.36, 70, 106, True, False, zMinPlot=0.2)
dataSampleList.append(newSample)
newSample = Sample(fullName = "lss.dr72lrgbright.dat",
nickName = "lrgbright",
dataType = "observation",
maskFile = inputDataDir+"/healpix/rast_window_512.fits",
selFunFile = inputDataDir+"/czselfunc.all.dr72lrgbright.dat",
zBoundary = (0.36, 0.44),
zRange = (0.36, 0.44),
skyFraction = 0.19,
minVoidRadius = 38,
fakeDensity = 0.001,
profileBinSize = "auto",
volumeLimited = True,
includeInHubble = False,
partOfCombo = False,
isCombo = False,
comboList= None)
newSample.addStack(0.36, 0.44, 76, 92, False, False)
newSample.addStack(0.36, 0.44, 92, 108, False, False)
dataSampleList.append(newSample)

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pipeline/datasets/example_simulation.py Normal file
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#+
# VIDE -- Void IDEntification pipeline -- ./pipeline/datasets/mergertree.py
# Copyright (C) 2010-2013 Guilhem Lavaux
# Copyright (C) 2011-2013 P. M. Sutter
#
# 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; version 2 of the License.
#
#
# 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 os
# -----------------------------------------------------------------------------
# -----------------------------------------------------------------------------
# CONFIGURATION
startCatalogStage = 0
endCatalogStage = 0
continueRun = False
startAPStage = 1
endAPStage = 2
# directory for the input simulation/observational particle files
catalogDir = os.getenv("HOME")+"/workspace/Voids/catalogs/mergertree1024/"
# path to HOD code
hodPath = os.getenv("HOME")+"/projects/Voids/hod/HOD.x"
# where to put the final void catalog, figures, and output logs
voidOutputDir = os.getenv("HOME")+"/workspace/Voids/mergertree1024/"
figDir = os.getenv("PWD")+"/../figs/mergertree1024/"
logDir = os.getenv("PWD")+"/../logs/mergertree1024/"
# where to place the pipeline scripts
scriptDir = os.getenv("PWD")+"/mergertree1024/"
# simulation or observation?
dataType = "simulation"
# available formats for simulation: gadget, mergertree
dataFormat = "sdf"
dataUnit = 1 # as multiple of Mpc/h
# place particles on the lightcone?
useLightCone = False
# also do peculiar velocities?
doPecVel = False
# common filename of particle files
particleFileBase = "mf_4s_1G_1k_NNNNN"
particleFileDummy = 'NNNNN'
# list of file numbers for the particle files
# to get particle file name, we take particleFileBase+fileNum
fileNums = ["1.000"]
# redshift of each file in the above list
redshifts = ["0.0"]
# how many independent slices along the z-axis?
numSlices = 1
#numSlices = 4
numAPSlices = 1
# how many subdivisions along the x- and y- axis?
# ( = 2 will make 4 subvolumes for each slice, = 3 will make 9, etc.)
numSubvolumes = 1
# prefix to give all outputs
prefix = "mt_"
# list of desired subsamples - these are in unts of h Mpc^-3!
subSamples = [0.1, 0.05, 0.02, 0.01, 0.004, 0.002, 0.001, 0.0003, 0.0001]
#doSubSampling = False # do the subsampling in preparation script?
doSubSampling = True # do the subsampling in preparation script?
# common filename of halo files, leave blank to ignore halos
haloFileBase = "mf_4s_1G_1k_bgc2_NNNNN.sdf"
haloFileDummy = 'NNNNN'
# minimum halo mass cuts to apply for the halo catalog
# use "none" to get all halos
minHaloMasses = ["none", 1.2e13]
#minHaloMasses = [7.0e11, 1.2e13]
# locations of data in the halo catalog
haloFileMCol = 6
haloFileXCol = 0
haloFileYCol = 1
haloFileZCol = 2
haloFileVXCol = 3
haloFileVYCol = 4
haloFileVZCol = 5
haloFileColSep = ','
haloFileNumComLines = 0
# adjust these two parameters given the memory contraints on your system:
# numZobovDivisions: how many sub-volumes per dimension will zobov process
# numZobovThreads: how many sub-volumes to process at once?
numZobovDivisions = 4
numZobovThreads = 4
# simulation information
numPart = 1024*1024*1024
lbox = 999.983 # Mpc/h
omegaM = 0.2847979853038958
hubble = 0.6962
#galDens = 0.000225
hodParmList = [
{'name' : "LowRes", #BOSS: Manera et al. 2012, eq. 26
'Mmin' : 0.0,
'M1' : 1.e14,
'sigma_logM' : 0.596,
'alpha' : 1.0127,
'Mcut' : 1.19399e13,
'galDens' : 0.0002,
},
{'name' : "HighRes",
'Mmin' : 0.0,
#'Mmin' : 1.99525e12,
'M1' : 3.80189e13,
'sigma_logM' : 0.21,
'alpha' : 1.12,
'Mcut' : 6.91831e11,
'galDens' : 0.02,
}
]
# END CONFIGURATION
# -----------------------------------------------------------------------------
# -----------------------------------------------------------------------------