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Merge branch 'master' of bitbucket.org:cosmicvoids/void_identification

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This commit is contained in:
Guilhem Lavaux 2013-03-05 14:23:21 +01:00
commit 33d0cfa302
8 changed files with 76 additions and 45 deletions
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2
c_tools/analysis/voidOverlap.cpp
View file

@ -286,7 +286,7 @@ int main(int argc, char **argv) {
rdist = catalog1.voids[iVoid1].matches[0].dist;
rdist /= catalog1.voids[iVoid1].radius;
fprintf(fp, "%d %.2f %.2f %.2f %.2f %.2f %d %d\n", voidID,
fprintf(fp, "%d %.4f %.4f %.4f %.4f %.4f %d %d\n", voidID,
catalog1.voids[iVoid1].radiusMpc,
rRatio,
commonVolRatio,

8
c_tools/mock/generateMock.cpp
View file

@ -370,7 +370,7 @@ void buildBox(SimuData *simu, long num_targets, long loaded,
for (uint32_t i = 0; i < num_targets; i++, loaded++)
{
long pid = particle_id[loaded];
assert(pid < simu->NumPart);
//assert(pid < simu->NumPart);
assert(loaded < boxed->NumPart);
for (int j = 0; j < 3; j++)
@ -545,6 +545,7 @@ void makeBoxFromParameter(SimuData *simu, SimuData* &boxed, generateMock_info& a
}
boxed->NumPart = pid_write;
delete preselect;
cout << "Num accepted here = " << pid_write << " / input = " << pid_read << endl;
}
void makeBoxFromSimulation(SimulationLoader *loader, SimuData* &boxed, MetricFunctor metric, generateMock_info& args_info)
@ -713,6 +714,9 @@ int main(int argc, char **argv)
args_info.output_arg);
delete preselector;
printf("Done!\n");
double subsample = 1.0;
if (args_info.subsample_given) subsample = args_info.subsample_arg;
if (args_info.resubsample_given) subsample = args_info.resubsample_arg;
printf("Done! %5.2e\n", subsample);
return 0;
}

14
crossCompare/analysis/datasetsToAnalyze.py
View file

@ -21,15 +21,23 @@
workDir = "/home/psutter2/workspace/Voids/"
dataDir = "/home/psutter2/workspace/Voids/multidark/crossCompare/mergerTree/"
dataDir = "/home/psutter2/workspace/Voids/crossCompare/mergerTree/"
CTOOLS_PATH = "../../c_tools/"
baseSampleDir = "multidark/md_ss0.000175/sample_md_ss0.000175_z0.56_d00/"
baseSampleDir = "multidark/md_ss0.05/sample_md_ss0.05_z0.56_d00/"
sampleDirList = [
"multidark/md_ss0.0004/sample_md_ss0.0004_z0.56_d00/",
"multidark/md_ss1e-05/sample_md_ss1e-05_z0.56_d00/",
#"multidark/md_ss0.000175/sample_md_ss0.000175_z0.56_d00/",
#"multidark/md_ss0.0004/sample_md_ss0.0004_z0.56_d00/",
#"multidark/md_ss0.001/sample_md_ss0.001_z0.56_d00/",
#"multidark/md_ss0.002/sample_md_ss0.002_z0.56_d00/",
"multidark/md_ss0.01/sample_md_ss0.01_z0.56_d00/",
"multidark/md_hod_dr72dim2/sample_md_hod_dr72dim2_z0.56_d00/",
"multidark/md_hod_dr9mid/sample_md_hod_dr9mid_z0.56_d00/",
"multidark/md_halos_min1.2e+13/sample_md_halos_min1.2e+13_z0.56_d00/",
]
dataPortion = "central"

8
crossCompare/analysis/mergerTree.py
View file

@ -63,6 +63,7 @@ for (iSample, sampleDir) in enumerate(sampleDirList):
sample = pickle.load(input)
print " Working with", sample.fullName, "...",
sys.stdout.flush()
sampleName = sample.fullName
@ -72,11 +73,12 @@ for (iSample, sampleDir) in enumerate(sampleDirList):
sampleName + "_"
#stepOutputFileName = os.getcwd()+"/data/overlap_"
launchVoidOverlap(baseSample, sample, workDir+baseSampleDir,
workDir+sampleDir, binPath,
launchVoidOverlap(sample, baseSample, workDir+sampleDir,
workDir+baseSampleDir, binPath,
thisDataPortion="central", logFile=logFile,
continueRun=False, workDir=workDir,
outputFile=stepOutputFileName)
outputFile=stepOutputFileName,
matchMethod="proximity")
# attach columns to summary file
#if iSample == 1:

23
pipeline/datasets/multidark.py
View file

@ -30,12 +30,12 @@ catalogDir = os.getenv("HOME")+"/workspace/Voids/catalogs/multidark/"
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/multidark_nocone/"
figDir = os.getenv("PWD")+"/../figs/multidark_nocone/"
logDir = os.getenv("PWD")+"/../logs/multidark_nocone/"
voidOutputDir = os.getenv("HOME")+"/workspace/Voids/multidark/"
figDir = os.getenv("PWD")+"/../figs/multidark/"
logDir = os.getenv("PWD")+"/../logs/multidark/"
# where to place the pipeline scripts
scriptDir = os.getenv("PWD")+"/multidark_nocone/"
scriptDir = os.getenv("PWD")+"/multidark/"
# simulation or observation?
dataType = "simulation"
@ -49,15 +49,19 @@ useLightCone = False
# common filename of particle files
particleFileBase = "mdr1_particles_z"
particleFileDummy = ''
# list of file numbers for the particle files
# to get particle file name, we take particleFileBase+fileNum
#fileNums = ["0.53"]
fileNums = ["0.0", "0.53", "1.0"]
fileNums = ["0.0"]
#fileNums = ["0.0", "0.53", "1.0"]
# redshift of each file in the above list
#redshifts = ["0.53"]
redshifts = ["0.0", "0.53", "1.0"]
redshifts = ["0.0"]
#redshifts = ["0.0", "0.53"]
#redshifts = ["0.0", "0.53", "1.0"]
# how many independent slices along the z-axis?
numSlices = 1
@ -71,7 +75,7 @@ numSubvolumes = 1
prefix = "md_"
# list of desired subsamples - these are in unts of h Mpc^-3!
#subSamples = [0.0004]
#subSamples = [0.01]
subSamples = [0.1, 0.05, 0.01, 0.002, 0.001, 0.0004, 0.000175, 0.00001]
# common filename of halo files, leave blank to ignore halos
@ -97,11 +101,12 @@ 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
numZobovDivisions = 2
numZobovThreads = 2
# simulation information
numPart = 2048*2048*2048
numPart = 100000000
#numPart = 2048*2048*2048
lbox = 1000 # Mpc/h
omegaM = 0.27
hubble = 0.70

4
pipeline/generateCatalog.py Normal file → Executable file
View file

@ -1,3 +1,4 @@
#!/usr/bin/env python
#+
# VIDE -- Void IDEntification pipeline -- ./pipeline/generateCatalog.py
# Copyright (C) 2010-2013 Guilhem Lavaux
@ -17,7 +18,6 @@
# 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 full void analysis. Also generates 2d/1d stacked plots and hubble diagram
@ -88,7 +88,7 @@ for sample in dataSampleList:
if (sample.dataType == "simulation"):
fp.write("Particles placed on lightcone: %g\n" % sample.useLightCone)
fp.write("Peculiar velocities included: %g\n" % sample.usePecVel)
fp.write("Additional subsampling fraction: %g\n" % sample.subsample)
fp.write("Additional subsampling fraction: %s\n" % sample.subsample[-1])
fp.write("Simulation box length (Mpc/h): %g\n" % sample.boxLen)
fp.write("Simulation Omega_M: %g\n" % sample.omegaM)
fp.write("Number of simulation subvolumes: %s\n" % sample.numSubvolumes)

3
python_tools/pipeline_source/prepareCatalogs.in.py
View file

@ -1,3 +1,4 @@
#!/usr/bin/env python
#+
# VIDE -- Void IDEntification pipeline -- ./python_tools/pipeline_source/prepareCatalogs.in.py
# Copyright (C) 2010-2013 Guilhem Lavaux
@ -17,7 +18,6 @@
# 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
# prepares input catalogs based on multidark simulations
# (borrows heavily from generateMock, but doesn't hold much in memory)
@ -453,6 +453,7 @@ if (args.halos or args.all) and haloFileBase != "":
if dataFormat == "sdf":
# TODO process halo file with SDFcvt
SDFcvt_PATH = "@CMAKE_BINARY_DIR@/ep_build/sdf/bin/SDFcvt/"
outFile = open(catalogDir+"/"+sampleName+".dat", 'w')
outFile.write("-99 -99 -99 -99 -99 -99 -99\n")
outFile.close()

55
python_tools/void_python_tools/backend/launchers.py
View file

@ -124,20 +124,31 @@ def launchGenerate(sample, binPath, workDir=None, inputDataDir=None,
datafile = inputDataDir+"/"+sample.dataFile
# check if the final subsampling is done
lastSample = sample.subsample.split(', ')[-1]
doneLine = "Done! %5.2e\n" % float(lastSample)
if (continueRun and jobSuccessful(logFile, doneLine)):
print "already done!"
return
prevSubSample = -1
for thisSubSample in sample.subsample.split(', '):
if prevSubSample == -1:
inputParameterFlag = ""
outputFile = zobovDir+"/zobov_slice_" + sampleName + "_ss" + thisSubSample
outputFile = zobovDir+"/zobov_slice_" + sampleName + "_ss" + \
thisSubSample
keepFraction = float(thisSubSample)
subSampleLine = "subsample %g" % keepFraction
resubSampleLine = ""
else:
inputParameterFlag = "inputParameter " + zobovDir+"/zobov_slice_"+\
sampleName+"_ss"+prevSubSample+".par"
outputFile = zobovDir+"/_zobov_slice_" + sampleName + "_ss" + thisSubSample
outputFile = zobovDir+"/zobov_slice_" + sampleName + "_ss" + \
thisSubSample
keepFraction = float(thisSubSample)/float(prevSubSample)
subSampleLine = "resubsample %g" % keepFraction
subSampleLine = "subsample %g" % keepFraction
resubSampleLine = "resubsample %g" % keepFraction
includePecVelString = ""
if sample.usePecVel: includePecVelString = "peculiarVelocities"
@ -175,6 +186,7 @@ def launchGenerate(sample, binPath, workDir=None, inputDataDir=None,
rangeZ_max %g
%s
%s
%s
""" % (dataFileLine, outputFile,
outputFile+".par",
includePecVelString,
@ -182,33 +194,30 @@ def launchGenerate(sample, binPath, workDir=None, inputDataDir=None,
sample.dataUnit,
xMin, xMax, yMin, yMax,
sample.zBoundaryMpc[0], sample.zBoundaryMpc[1],
subSampleLine,inputParameterFlag)
subSampleLine,resubSampleLine,inputParameterFlag)
parmFile = os.getcwd()+"/generate_"+sample.fullName+".par"
file(parmFile, mode="w").write(conf)
doneLine = "Done! %5.2e\n" % keepFraction
print "TEST", doneLine
if not (continueRun and jobSuccessful(logFile, doneLine)):
if (prevSubSample == -1):
cmd = "%s --configFile=%s &> %s" % (binPath,parmFile,logFile)
else:
cmd = "%s --configFile=%s &>> %s" % (binPath,parmFile,logFile)
os.system(cmd)
if not jobSuccessful(logFile, doneLine):
print "FAILED!"
exit(-1)
if (prevSubSample == -1):
cmd = "%s --configFile=%s &> %s" % (binPath,parmFile,logFile)
else:
cmd = "%s --configFile=%s &>> %s" % (binPath,parmFile,logFile)
os.system(cmd)
# remove intermediate files
if (prevSubSample != -1):
os.unlink(zobovDir+"/zobov_slice_"+sampleName+"_ss"+prevSubSample+".par")
os.unlink(zobovDir+"/zobov_slice_"+sampleName+"_ss"+prevSubSample)
doneLine = "Done! %5.2e\n" % keepFraction
if not jobSuccessful(logFile, doneLine):
print "FAILED!"
exit(-1)
prevSubSample = thisSubSample
if (continueRun and jobSuccessful(logFile, doneLine)): print "already done!"
if jobSuccessful(logFile, doneLine): print "done"
# place the final subsample
@ -690,7 +699,7 @@ def launchCombine(sample, stack, voidDir=None, logFile=None,
shutil.copy(workDir+"/sample_"+comboName+"/galaxies.txt", zobovDir)
elif not doneGalUpdate:
dataTemp = file(workDir+"/sample_"+comboName+"/galaxies.txt",
"r").read()
"r").read()
file(zobovDir+"/galaxies.txt", "a").write(dataTemp)
sourceStackDir = workDir+"/sample_"+comboName+"/stacks_"+\
@ -758,8 +767,9 @@ def launchCombine(sample, stack, voidDir=None, logFile=None,
idxTemp = file(sourceStackDir+"/z_void_indexes.txt", "r").\
readlines()
idxTemp = np.array(idxTemp, dtype='i')
dataTemp = (NetCDFFile(voidDir+"/z_posx.nc").\
variables['array'])[0:]
fp = NetCDFFile(voidDir+"/z_posx.nc")
dataTemp = fp.variables['array'][0:]
fp.close()
idxTemp[:] += len(dataTemp)
fp = open(voidDir+"/z_void_indexes.txt", "a")
for idx in idxTemp:
@ -809,8 +819,9 @@ def launchCombine(sample, stack, voidDir=None, logFile=None,
idxTemp = file(sourceStackDir+"/void_indexes.txt", "r").\
readlines()
idxTemp = np.array(idxTemp, dtype='i')
dataTemp = (NetCDFFile(voidDir+"/posx.nc").\
variables['array'])[0:]
fp = NetCDFFile(voidDir+"/posx.nc")
dataTemp = fp.variables['array'][0:]
fp.close()
idxTemp[:] += len(dataTemp)
fp = open(voidDir+"/void_indexes.txt", "a")
for idx in idxTemp: