bug fixes

python_tools/setup.py

@@ -31,7 +31,7 @@ setup(
     cmdclass = {'build_ext': build_ext},
     include_dirs = [np.get_include()],
     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',],
     #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 = [

python_tools/void_python_tools/voidUtil/catalogUtil.py

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

python_tools/void_python_tools/voidUtil/matchUtil.py

@@ -32,7 +32,7 @@ def compareCatalogs(baseCatalogDir, compareCatalogDir,
                     outputDir="./", logDir="./", 
                     matchMethod="useID", dataPortion="central",
                     strictMatch=True, 
-                    pathToCTools="../../../c_tools")
+                    pathToCTools="../../../c_tools"):
 
 # reports the overlap between two void catalogs
 #  baseCatalogDir: directory of catalog 1
@@ -44,36 +44,37 @@ def compareCatalogs(baseCatalogDir, compareCatalogDir,
 #  strictMatch: if True, only attempt to match to trimmed catalog
 #  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,
-                  outputFile=stepOutputFileName,
+                    outputFile=stepOutputFileName,
-                  matchMethod=matchMethod,
+                    matchMethod=matchMethod,
-                  strictMatch=strictMatch)
+                    strictMatch=strictMatch)
-
+  
-print " Done!"
+  print " Done!"
+  return

python_tools/void_python_tools/voidUtil/plotUtil.py

@@ -43,68 +43,68 @@ def plotNumberFunction(catalogList, figDir="./",
                        plotName="numberfunc", 
                        dataPortion="central"):
 
-print "Plotting number function"
+  print "Plotting number function"
-
-plt.clf()
-plt.xlabel("$R_{eff}$ [$h^{-1}Mpc$]", fontsize=14)
-plt.ylabel(r"log ($n$ (> R) [$h^3$ Gpc$^{-3}$])", fontsize=14)
-
-for (iSample,catalog) in enumerate(catalogList):
-  sample = catalog.sampleInfo
-  data = catalog.voids[:].radius
-
-  if sample.dataType == "observation":
-    maskFile = sample.maskFile
-
-    boxVol = vp.getSurveyProps(maskFile,
-                               sample.zBoundary[0], sample.zBoundary[1],
-                               sample.zRange[0], sample.zRange[1], "all",
-                               selectionFuncFile=None)[0]
-                               #selectionFuncFile=sample.selFunFile)[0]
-    boxVol *= obsFudgeFactor
-  else:
-    boxVol = sample.boxLen*sample.boxLen*(sample.zBoundaryMpc[1] -
-                                          sample.zBoundaryMpc[0])
-
-  boxVol *= 1.e-9 # Mpc->Gpc
-
-  bins = args.xmax/5.
-  hist, binEdges = np.histogram(data, bins=bins, range=(0., 100.))
-  binCenters = 0.5*(binEdges[1:] + binEdges[:-1])
-
-  nvoids = len(data)
-  var = hist * (1. - hist/nvoids)
-  sig = np.sqrt(var)
-
-  lowerbound = hist - sig
-  upperbound = hist + sig
-
-  mean = np.log10(hist/boxVol)
-  lowerbound = np.log10(lowerbound/boxVol)
-  upperbound = np.log10(upperbound/boxVol)
-
-  lineColor = colorList[iSample]
-  lineTitle = sample.fullName
   
-  trim = (bounds[0] > .01)
+  plt.clf()
-  mean = mean[trim]
+  plt.xlabel("$R_{eff}$ [$h^{-1}Mpc$]", fontsize=14)
-  binCentersToUse = binCenters[trim]
+  plt.ylabel(r"log ($n$ (> R) [$h^3$ Gpc$^{-3}$])", fontsize=14)
-  lower = lowerbound[trim]
+  
-  upper = upperbound[trim]
+  for (iSample,catalog) in enumerate(catalogList):
-
+    sample = catalog.sampleInfo
-  alpha = 0.55
+    data = catalog.voids[:].radius
-  fill_between(binCentersToUse, lower, upper,
+  
-             label=lineTitle, color=lineColor,
+    if sample.dataType == "observation":
-             alpha=alpha,
+      maskFile = sample.maskFile
-             )
+  
-
+      boxVol = vp.getSurveyProps(maskFile,
-  lineStyle = '-'
+                                 sample.zBoundary[0], sample.zBoundary[1],
-  plt.plot(binCentersToUse, mean, lineStyle,
+                                 sample.zRange[0], sample.zRange[1], "all",
-              color=lineColor,
+                                 selectionFuncFile=None)[0]
-              linewidth=3)
+                                 #selectionFuncFile=sample.selFunFile)[0]
-
+      boxVol *= obsFudgeFactor
-  plt.legend(loc = "upper right", fancybox=True, prop={'size':14})
+    else:
-
+      boxVol = sample.boxLen*sample.boxLen*(sample.zBoundaryMpc[1] -
-  plt.savefig(figDir+"/fig_"+plotName+".pdf", bbox_inches="tight")
+                                            sample.zBoundaryMpc[0])
-  plt.savefig(figDir+"/fig_"+plotName+".eps", bbox_inches="tight")
+  
-  plt.savefig(figDir+"/fig_"+plotName+".png", bbox_inches="tight")
+    boxVol *= 1.e-9 # Mpc->Gpc
+  
+    bins = args.xmax/5.
+    hist, binEdges = np.histogram(data, bins=bins, range=(0., 100.))
+    binCenters = 0.5*(binEdges[1:] + binEdges[:-1])
+  
+    nvoids = len(data)
+    var = hist * (1. - hist/nvoids)
+    sig = np.sqrt(var)
+  
+    lowerbound = hist - sig
+    upperbound = hist + sig
+  
+    mean = np.log10(hist/boxVol)
+    lowerbound = np.log10(lowerbound/boxVol)
+    upperbound = np.log10(upperbound/boxVol)
+  
+    lineColor = colorList[iSample]
+    lineTitle = sample.fullName
+    
+    trim = (bounds[0] > .01)
+    mean = mean[trim]
+    binCentersToUse = binCenters[trim]
+    lower = lowerbound[trim]
+    upper = upperbound[trim]
+  
+    alpha = 0.55
+    fill_between(binCentersToUse, lower, upper,
+               label=lineTitle, color=lineColor,
+               alpha=alpha,
+               )
+  
+    lineStyle = '-'
+    plt.plot(binCentersToUse, mean, lineStyle,
+                color=lineColor,
+                linewidth=3)
+  
+    plt.legend(loc = "upper right", fancybox=True, prop={'size':14})
+  
+    plt.savefig(figDir+"/fig_"+plotName+".pdf", bbox_inches="tight")
+    plt.savefig(figDir+"/fig_"+plotName+".eps", bbox_inches="tight")
+    plt.savefig(figDir+"/fig_"+plotName+".png", bbox_inches="tight")

python_tools/void_python_tools/voidUtil/profileUtil.py

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

python_tools/void_python_tools/voidUtil/xcorUtil.py

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