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bug fixes

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This commit is contained in:
P.M. Sutter 2014-05-09 12:01:59 -05:00
parent 4cf0ec1173
commit 39e16d41ff
6 changed files with 103 additions and 102 deletions
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2
python_tools/setup.py
View file

@ -31,7 +31,7 @@ setup(
cmdclass = {'build_ext': build_ext}, cmdclass = {'build_ext': build_ext},
include_dirs = [np.get_include()], include_dirs = [np.get_include()],
packages= packages=
['void_python_tools','void_python_tools.backend','void_python_tools.apTools', 'void_python_tools.xcor', 'void_python_tools.voidUtil', ['void_python_tools','void_python_tools.backend','void_python_tools.apTools', 'void_python_tools.voidUtil',
'void_python_tools.apTools.profiles','void_python_tools.apTools.chi2',], 'void_python_tools.apTools.profiles','void_python_tools.apTools.chi2',],
#ext_modules = [Extension("void_python_tools.chi2.velocityProfileFitNative", ["void_python_tools/chi2/velocityProfileFitNative.pyx"], libraries=["gsl", "gslcblas"]), Extension("void_python_tools.chi2.likelihoo", ["void_python_tools/chi2/likelihood.pyx"], libraries=["gsl", "gslcblas"])] #ext_modules = [Extension("void_python_tools.chi2.velocityProfileFitNative", ["void_python_tools/chi2/velocityProfileFitNative.pyx"], libraries=["gsl", "gslcblas"]), Extension("void_python_tools.chi2.likelihoo", ["void_python_tools/chi2/likelihood.pyx"], libraries=["gsl", "gslcblas"])]
#ext_modules = [ #ext_modules = [

2
python_tools/void_python_tools/voidUtil/catalogUtil.py
View file

@ -269,7 +269,7 @@ def loadVoidCatalog(sampleDir, dataPortion="central", loadPart=True):
densCon = line[9], densCon = line[9],
voidProb = line[10], voidProb = line[10],
radius = pow(line[7]/volNorm*3./4./np.pi, 1./3.), radius = pow(line[7]/volNorm*3./4./np.pi, 1./3.),
barycenter = np.zeros((3)) barycenter = np.zeros((3)),
parentID = 0, parentID = 0,
treeLevel = 0, treeLevel = 0,
numChildren = 0, numChildren = 0,

29
python_tools/void_python_tools/voidUtil/matchUtil.py
View file

@ -32,7 +32,7 @@ def compareCatalogs(baseCatalogDir, compareCatalogDir,
outputDir="./", logDir="./", outputDir="./", logDir="./",
matchMethod="useID", dataPortion="central", matchMethod="useID", dataPortion="central",
strictMatch=True, strictMatch=True,
pathToCTools="../../../c_tools") pathToCTools="../../../c_tools"):
# reports the overlap between two void catalogs # reports the overlap between two void catalogs
# baseCatalogDir: directory of catalog 1 # baseCatalogDir: directory of catalog 1
@ -44,31 +44,31 @@ def compareCatalogs(baseCatalogDir, compareCatalogDir,
# strictMatch: if True, only attempt to match to trimmed catalog # strictMatch: if True, only attempt to match to trimmed catalog
# pathToCTools: path to location of VIDE c_tools directory # pathToCTools: path to location of VIDE c_tools directory
if not os.access(outputDir, os.F_OK): if not os.access(outputDir, os.F_OK):
os.makedirs(outputDir) os.makedirs(outputDir)
if not os.access(logDir, os.F_OK): if not os.access(logDir, os.F_OK):
os.makedirs(logDir) os.makedirs(logDir)
outFileName = outputDir + "/" + "voidOverlap" #+ ".dat" outFileName = outputDir + "/" + "voidOverlap" #+ ".dat"
with open(baseCatalogDir+"/sample_info.dat", 'rb') as input: with open(baseCatalogDir+"/sample_info.dat", 'rb') as input:
baseSample = pickle.load(input) baseSample = pickle.load(input)
with open(compareCatalogDir+"/sample_info.dat", 'rb') as input: with open(compareCatalogDir+"/sample_info.dat", 'rb') as input:
sample = pickle.load(input) sample = pickle.load(input)
print " Comparing", baseSample.fullName, "to", sample.fullName, "...", print " Comparing", baseSample.fullName, "to", sample.fullName, "...",
sys.stdout.flush() sys.stdout.flush()
sampleName = sample.fullName sampleName = sample.fullName
binPath = pathToCTools+"/analysis/voidOverlap" binPath = pathToCTools+"/analysis/voidOverlap"
logFile = logDir+"/compare_"+baseSample.fullName+"_"+sampleName+".out" logFile = logDir+"/compare_"+baseSample.fullName+"_"+sampleName+".out"
stepOutputFileName = outFileName + "_" + baseSample.fullName + "_" + \ stepOutputFileName = outFileName + "_" + baseSample.fullName + "_" + \
sampleName + "_" sampleName + "_"
launchVoidOverlap(baseSample, sample, baseCatalogDir, launchVoidOverlap(baseSample, sample, baseCatalogDir,
compareCatalogDir, binPath, compareCatalogDir, binPath,
thisDataPortion=dataPortion, logFile=logFile, thisDataPortion=dataPortion, logFile=logFile,
continueRun=False, workDir=workDir, continueRun=False, workDir=workDir,
@ -76,4 +76,5 @@ launchVoidOverlap(baseSample, sample, baseCatalogDir,
matchMethod=matchMethod, matchMethod=matchMethod,
strictMatch=strictMatch) strictMatch=strictMatch)
print " Done!" print " Done!"
return

10
python_tools/void_python_tools/voidUtil/plotUtil.py
View file

@ -43,13 +43,13 @@ def plotNumberFunction(catalogList, figDir="./",
plotName="numberfunc", plotName="numberfunc",
dataPortion="central"): dataPortion="central"):
print "Plotting number function" print "Plotting number function"
plt.clf() plt.clf()
plt.xlabel("$R_{eff}$ [$h^{-1}Mpc$]", fontsize=14) plt.xlabel("$R_{eff}$ [$h^{-1}Mpc$]", fontsize=14)
plt.ylabel(r"log ($n$ (> R) [$h^3$ Gpc$^{-3}$])", fontsize=14) plt.ylabel(r"log ($n$ (> R) [$h^3$ Gpc$^{-3}$])", fontsize=14)
for (iSample,catalog) in enumerate(catalogList): for (iSample,catalog) in enumerate(catalogList):
sample = catalog.sampleInfo sample = catalog.sampleInfo
data = catalog.voids[:].radius data = catalog.voids[:].radius

2
python_tools/void_python_tools/voidUtil/profileUtil.py
View file

@ -94,7 +94,7 @@ def fitHSWProfile(radii, densities, sigmas):
# pcov: covariance matrix # pcov: covariance matrix
popt, pcov = curve_fit(HamausProfile, radii, densities, popt, pcov = curve_fit(HamausProfile, radii, densities,
sigma=sigmas) sigma=sigmas,
maxfev=10000, xtol=5.e-3, maxfev=10000, xtol=5.e-3,
p0=[1.0,-1.0]) p0=[1.0,-1.0])

2
python_tools/void_python_tools/voidUtil/xcorUtil.py
View file

@ -61,7 +61,7 @@ def computeCrossCor(catalogDir,
outputDir="./", logDir="./", outputDir="./", logDir="./",
matchMethod="useID", dataPortion="central", matchMethod="useID", dataPortion="central",
strictMatch=True, strictMatch=True,
pathToCTools="../../../c_tools") pathToCTools="../../../c_tools"):
# Computes void-void and void-matter(galaxy) correlations # Computes void-void and void-matter(galaxy) correlations
# baseCatalogDir: directory of catalog # baseCatalogDir: directory of catalog