mirror of
https://bitbucket.org/cosmicvoids/vide_public.git
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removal of some cross-comparison scripts
This commit is contained in:
P.M. Sutter
parent
4d6e653bda
commit
41e179da64
5 changed files with 0 additions and 495 deletions
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@ -1,129 +0,0 @@
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#!/usr/bin/env python
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#+
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# VIDE -- Void IDEntification pipeline -- ./pipeline/apAnalysis.py
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# Copyright (C) 2010-2013 Guilhem Lavaux
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# Copyright (C) 2011-2013 P. M. Sutter
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#
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# This program is free software; you can redistribute it and/or modify
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# it under the terms of the GNU General Public License as published by
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# the Free Software Foundation; version 2 of the License.
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#
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#
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# This program is distributed in the hope that it will be useful,
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# but WITHOUT ANY WARRANTY; without even the implied warranty of
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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# GNU General 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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#+
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# takes a set of voids with given radii, and stacks and plots matches in
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# other catalogs
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from void_python_tools.backend import *
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import imp
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import pickle
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import os
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import numpy as np
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import argparse
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# ------------------------------------------------------------------------------
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mergerNameBase = "mergerTree"
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parser = argparse.ArgumentParser(description='Analyze.')
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parser.add_argument('--parm', dest='parm', default='datasetsToAnalyze.py', help='path to parameter file')
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args = parser.parse_args()
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# ------------------------------------------------------------------------------
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filename = args.parm
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print " Loading parameters from", filename
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if not os.access(filename, os.F_OK):
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print " Cannot find parameter file %s!" % filename
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exit(-1)
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parms = imp.load_source("name", filename)
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globals().update(vars(parms))
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if not os.access(dataDir, os.F_OK):
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os.makedirs(dataDir)
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if not os.access(logDir, os.F_OK):
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os.makedirs(logDir)
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mergerFileBase = dataDir + "/" + mergerNameBase
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# get list of base voids
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with open(workDir+baseSampleDir+"/sample_info.dat", 'rb') as input:
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baseSample = pickle.load(input)
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baseSampleName = baseSample.fullName
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baseVoidList = np.loadtxt(workDir+baseSampleDir+"/untrimmed_centers_central_"+\
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baseSampleName+".out")
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for stack in baseSample.stacks:
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print " Stack:", stack.rMin
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accepted = (baseVoidList[:,4] > stack.rMin) & (baseVoidList[:,4] < stack.rMax)
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baseIDList = baseVoidList[:,7][accepted]
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for (iSample, sampleDir) in enumerate(sampleDirList):
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with open(workDir+sampleDir+"/sample_info.dat", 'rb') as input:
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sample = pickle.load(input)
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print " Working with", sample.fullName, "..."
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sys.stdout.flush()
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sampleName = sample.fullName
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# get list of appropriate voids
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if sample.fullName == baseSample.fullName:
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idList = baseIDList
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else:
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matchList = np.loadtxt(mergerFileBase+"_"+baseSampleName+"_"+sampleName+\
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"_summary.out")
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idList = []
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for i,testID in enumerate(matchList[:,8]):
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if np.any(testID == baseIDList):
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idList.append(matchList[i,0])
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idList = np.array(idList)
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idList = idList.astype(int)
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print " Found", len(idList), "voids to work with"
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voidBaseDir = workDir+"/"+sampleDir+"stacks"
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runSuffix = getStackSuffix(stack.zMin, stack.zMax, stack.rMin,
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stack.rMax, dataPortion,
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customLine="selected")
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voidDir = voidBaseDir+"_"+runSuffix
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if not os.access(voidDir,os.F_OK): os.makedirs(voidDir)
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if len(idList) == 0:
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print " No voids here anyway, skipping..."
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continue
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print " Stacking voids...",
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sys.stdout.flush()
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STACK_PATH = CTOOLS_PATH+"/stacking/stackVoidsZero"
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launchStack(sample, stack, STACK_PATH,
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thisDataPortion=dataPortion,
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logDir=logDir, voidDir=voidDir,
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zobovDir=workDir+"/"+sampleDir,
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freshStack=True, INCOHERENT=False,
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ranSeed=101010, summaryFile=None,
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continueRun=False,
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dataType=sample.dataType,
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idList=idList, rescaleOverride="")
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print " Profiling stacks...",
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sys.stdout.flush()
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logFile = logDir+"/profile_"+sampleName+"_"+runSuffix+".out"
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launchProfile(sample, stack, voidDir=voidDir,
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logFile=logFile, continueRun=False)
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print " Done!"
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@ -1,44 +0,0 @@
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#+
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# VIDE -- Void IDEntification pipeline -- ./crossCompare/analysis/datasetsToAnalyze.py
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# Copyright (C) 2010-2013 Guilhem Lavaux
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# Copyright (C) 2011-2013 P. M. Sutter
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#
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# This program is free software; you can redistribute it and/or modify
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# it under the terms of the GNU General Public License as published by
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# the Free Software Foundation; version 2 of the License.
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#
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#
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# This program is distributed in the hope that it will be useful,
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# but WITHOUT ANY WARRANTY; without even the implied warranty of
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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# GNU General 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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#+
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#!/usr/bin/env python
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workDir = "/home/psutter2/workspace/Voids/"
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dataDir = "/home/psutter2/workspace/Voids/crossCompare/mergerTree/"
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CTOOLS_PATH = "../../c_tools/"
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baseSampleDir = "mergertree512/mt_ss0.1/sample_md_ss0.1_z0.00_d00/"
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sampleDirList = [
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"mergertree512/mt_ss1e-05/sample_md_ss1e-05_z0.00_d00/",
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#"mergertree512/mt_ss0.000175/sample_md_ss0.000175_z0.00_d00/",
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#"mergertree512/mt_ss0.0004/sample_md_ss0.0004_z0.00_d00/",
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#"mergertree512/mt_ss0.001/sample_md_ss0.001_z0.00_d00/",
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#"mergertree512/mt_ss0.002/sample_md_ss0.002_z0.00_d00/",
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"mergertree512/mt_ss0.01/sample_md_ss0.01_z0.00_d00/",
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"mergertree512/mt_hod_dr72dim2/sample_md_hod_dr72dim2_z0.00_d00/",
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"mergertree512/mt_hod_dr9mid/sample_md_hod_dr9mid_z0.00_d00/",
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"mergertree512/mt_halos_min1.2e+13/sample_md_halos_min1.2e+13_z0.00_d00/",
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]
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dataPortion = "central"
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@ -1,104 +0,0 @@
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#!/usr/bin/env python
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#+
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# VIDE -- Void IDEntification pipeline -- ./crossCompare/analysis/mergerTree.py
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# Copyright (C) 2010-2013 Guilhem Lavaux
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# Copyright (C) 2011-2013 P. M. Sutter
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#
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# This program is free software; you can redistribute it and/or modify
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# it under the terms of the GNU General Public License as published by
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# the Free Software Foundation; version 2 of the License.
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#
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#
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# This program is distributed in the hope that it will be useful,
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# but WITHOUT ANY WARRANTY; without even the implied warranty of
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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# GNU General 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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#+
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from void_python_tools.backend import *
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from void_python_tools.plotting import *
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import imp
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import pickle
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import os
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import matplotlib.pyplot as plt
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import numpy as np
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import argparse
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# ------------------------------------------------------------------------------
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dataNameBase = "mergerTree"
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parser = argparse.ArgumentParser(description='Analyze.')
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parser.add_argument('--parm', dest='parm', default='datasetsToAnalyze.py',
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help='path to parameter file')
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args = parser.parse_args()
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# ------------------------------------------------------------------------------
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filename = args.parm
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print " Loading parameters from", filename
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if not os.access(filename, os.F_OK):
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print " Cannot find parameter file %s!" % filename
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exit(-1)
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parms = imp.load_source("name", filename)
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globals().update(vars(parms))
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if not os.access(dataDir, os.F_OK):
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os.makedirs(dataDir)
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outFileName = dataDir + "/" + dataNameBase #+ ".dat"
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with open(workDir+baseSampleDir+"/sample_info.dat", 'rb') as input:
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baseSample = pickle.load(input)
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for (iSample, sampleDir) in enumerate(sampleDirList):
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with open(workDir+sampleDir+"/sample_info.dat", 'rb') as input:
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sample = pickle.load(input)
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print " Working with", sample.fullName, "...",
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sys.stdout.flush()
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sampleName = sample.fullName
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binPath = CTOOLS_PATH+"/analysis/voidOverlap"
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logFile = logDir+"/mergertree_"+baseSample.fullName+"_"+sampleName+".out"
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stepOutputFileName = outFileName + "_" + baseSample.fullName + "_" + \
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sampleName + "_"
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#stepOutputFileName = os.getcwd()+"/data/overlap_"
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launchVoidOverlap(sample, baseSample, workDir+sampleDir,
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workDir+baseSampleDir, binPath,
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thisDataPortion="central", logFile=logFile,
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continueRun=False, workDir=workDir,
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outputFile=stepOutputFileName,
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matchMethod="useID")
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#matchMethod="prox")
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# attach columns to summary file
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#if iSample == 1:
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# os.system("cp %s %s" % (stepOutputFileName, outFileName))
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#else:
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# outFile = open("temp.out", "w")
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# stepOutFile1 = open(outFileName, "r")
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# stepOutFile2 = open(stepOutputFileName, "r")
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#
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# for line1 in stepOutFile1:
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# line1 = line1.rstrip()
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# line2 = stepOutFile2.readline()
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# outFile.write(line1+" "+line2)
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#
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# os.system("cp %s %s" % ("temp.out", outFileName))
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# outFile.close()
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# stepOutFile1.close()
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# stepOutFile2.close()
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#if os.access("mergerTree.log", os.F_OK): os.unlink("mergerTree.log")
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#if os.access("temp.out", os.F_OK): os.unlink("temp.out")
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#if os.access("thisStep.out", os.F_OK): os.unlink("thisStep.out")
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print " Done!"
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#+
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# VIDE -- Void IDEntification pipeline -- ./pipeline/datasets/mock_dr9mid.py
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# Copyright (C) 2010-2013 Guilhem Lavaux
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# Copyright (C) 2011-2013 P. M. Sutter
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#
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# This program is free software; you can redistribute it and/or modify
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# it under the terms of the GNU General Public License as published by
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# the Free Software Foundation; version 2 of the License.
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#
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#
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# This program is distributed in the hope that it will be useful,
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# but WITHOUT ANY WARRANTY; without even the implied warranty of
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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# GNU General 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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#+
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import os
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# -----------------------------------------------------------------------------
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# -----------------------------------------------------------------------------
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# CONFIGURATION
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# directory for the input simulation/observational particle files
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catalogDir = os.getenv("HOME")+"/workspace/Voids/catalogs/mock_dr9mid/"
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# path to HOD code
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hodPath = os.getenv("HOME")+"/projects/Voids/hod/HOD.x"
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# path to mask
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maskFile = os.getenv("HOME")+"/workspace/Voids/catalogs/boss/final_boss_mask.fits")
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# where to put the final void catalog, figures, and output logs
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voidOutputDir = os.getenv("HOME")+"/workspace/Voids/mock_dr9mid/"
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figDir = os.getenv("PWD")+"/../figs/mock_dr9mid/"
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logDir = os.getenv("PWD")+"/../logs/mock_dr9mid/"
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# where to place the pipeline scripts
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scriptDir = os.getenv("PWD")+"/mock_dr9mid/"
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# simulation or observation?
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dataType = "observation"
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# available formats for simulation: gadget, multidark
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dataFormat = "multidark"
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dataUnit = 1 # as multiple of Mpc/h
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# place particles on the lightcone?
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useLightCone = True
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# list of file numbers for the particle files
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# to get particle file name, we take particleFileBase+fileNum
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fileNums = (("0.53"))
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# redshift range of the mock
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redshiftRange = (0.53, 0.6)
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# prefix to give all outputs
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prefix = "mock_"
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# common filename of halo files
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haloFileBase = "mdr1_halos_z"
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# adjust these two parameters given the memory contraints on your system:
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# numZobovDivisions: how many sub-volumes per dimension will zobov process
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# numZobovThreads: how many sub-volumes to process at once?
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numZobovDivisions = 2
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numZobovThreads = 2
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# simulation information
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numPart = 1024*1024*1024
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lbox = 1000 # Mpc/h
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omegaM = 0.27
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hubble = 0.70
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# END CONFIGURATION
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# -----------------------------------------------------------------------------
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# -----------------------------------------------------------------------------
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@ -1,137 +0,0 @@
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#+
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# VIDE -- Void IDEntification pipeline -- ./pipeline/datasets/multidark.py
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# Copyright (C) 2010-2013 Guilhem Lavaux
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# Copyright (C) 2011-2013 P. M. Sutter
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#
|
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# 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.
|
||||
#
|
||||
#
|
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# 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.
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#+
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import os
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# -----------------------------------------------------------------------------
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# -----------------------------------------------------------------------------
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# CONFIGURATION
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# directory for the input simulation/observational particle files
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catalogDir = os.getenv("HOME")+"/workspace/Voids/catalogs/multidark/"
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# path to HOD code
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hodPath = os.getenv("HOME")+"/projects/Voids/hod/HOD.x"
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# where to put the final void catalog, figures, and output logs
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voidOutputDir = os.getenv("HOME")+"/workspace/Voids/multidark/"
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figDir = os.getenv("PWD")+"/../figs/multidark/"
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logDir = os.getenv("PWD")+"/../logs/multidark/"
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# where to place the pipeline scripts
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scriptDir = os.getenv("PWD")+"/multidark/"
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# simulation or observation?
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dataType = "simulation"
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# available formats for simulation: gadget, multidark
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dataFormat = "multidark"
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dataUnit = 1 # as multiple of Mpc/h
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# place particles on the lightcone?
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useLightCone = False
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# common filename of particle files
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particleFileBase = "mdr1_particles_z"
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particleFileDummy = ''
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# list of file numbers for the particle files
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# to get particle file name, we take particleFileBase+fileNum
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#fileNums = ["0.53"]
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fileNums = ["0.0"]
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#fileNums = ["0.0", "0.53", "1.0"]
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# redshift of each file in the above list
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#redshifts = ["0.53"]
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redshifts = ["0.0"]
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#redshifts = ["0.0", "0.53"]
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#redshifts = ["0.0", "0.53", "1.0"]
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# how many independent slices along the z-axis?
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numSlices = 1
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#numSlices = 4
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# how many subdivisions along the x- and y- axis?
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# ( = 2 will make 4 subvolumes for each slice, = 3 will make 9, etc.)
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numSubvolumes = 1
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# prefix to give all outputs
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prefix = "md_"
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# list of desired subsamples - these are in unts of h Mpc^-3!
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#subSamples = [0.01]
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subSamples = [0.1, 0.05, 0.01, 0.002, 0.001, 0.0004, 0.000175, 0.00001]
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# common filename of halo files, leave blank to ignore halos
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haloFileBase = "mdr1_halos_z"
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haloFileDummy = ''
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# minimum halo mass cuts to apply for the halo catalog
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# use "none" to get all halos
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minHaloMasses = [1.2e13]
|
||||
#minHaloMasses = ["none", 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 = 2
|
||||
numZobovThreads = 2
|
||||
|
||||
# simulation information
|
||||
numPart = 100000000
|
||||
#numPart = 2048*2048*2048
|
||||
lbox = 1000 # Mpc/h
|
||||
omegaM = 0.27
|
||||
hubble = 0.70
|
||||
|
||||
#galDens = 0.000225
|
||||
hodParmList = [
|
||||
{'name' : "dr9mid", #BOSS: Manera et al. 2012, eq. 26
|
||||
'Mmin' : 0.0,
|
||||
'M1' : 1.e14,
|
||||
'sigma_logM' : 0.596,
|
||||
'alpha' : 1.0127,
|
||||
'Mcut' : 1.19399e13,
|
||||
'galDens' : 0.00016,
|
||||
},
|
||||
|
||||
{'name' : "dr7dim2",
|
||||
'Mmin' : 1.99525e12,
|
||||
'M1' : 3.80189e13,
|
||||
'sigma_logM' : 0.21,
|
||||
'alpha' : 1.12,
|
||||
'Mcut' : 6.91831e11,
|
||||
'galDens' : 0.02,
|
||||
}
|
||||
]
|
||||
|
||||
# END CONFIGURATION
|
||||
# -----------------------------------------------------------------------------
|
||||
# -----------------------------------------------------------------------------
|
||||
Loading…
Add table
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Reference in a new issue