central density calculation now uses correct normalization from survey volume

python_source/backend/classes.py

@@ -88,6 +88,8 @@ class Sample:
   includeInHubble = True
   partOfCombo  = False
   isCombo = False
+  volNormZobov = 0
+  volNormObs = 0
   
   comboList = []
 

python_source/backend/launchers.py

@@ -608,6 +608,8 @@ def launchPrune(sample, binPath,
   else:
     minRadius = sample.minVoidRadius
 
+  volNormZobov, volNormObs = getVolNorm(sample)
+
   if not (continueRun and (jobSuccessful(logFile, "NetCDF: Not a valid ID\n") \
           or jobSuccessful(logFile, "Done!\n"))):
     cmd = binPath
@@ -626,6 +628,8 @@ def launchPrune(sample, binPath,
     cmd += volFileLine
     cmd += useComovingFlag
     cmd += " --omegaM=" + str(sample.omegaM)
+    cmd += " --volNormZobov=" + str(volNormZobov)
+    cmd += " --volNormObs=" + str(volNormObs)
     cmd += " --outputDir=" + outputDir
     cmd += " --sampleName=" + str(sampleName)
     log = open(logFile, 'w')

python_source/backend/surveyTools.py

@@ -27,7 +27,11 @@ import os
 from backend import *
 from backend.cosmologyTools import *
 
-__all__=['getSurveyProps', 'getNside', 'figureOutMask', 'findEdgeGalaxies']
+from netCDF4 import Dataset
+NetCDFFile = Dataset
+ncFloat = 'f8'
+
+__all__=['getSurveyProps', 'getVolNorm', 'getNside', 'figureOutMask', 'findEdgeGalaxies']
 
 # -----------------------------------------------------------------------------
 # returns the survey volume and scaled galaxy density for a given redshit slice
@@ -93,6 +97,60 @@ def getSurveyProps(sample):
   return (volume, nbar)
 
 
+# -----------------------------------------------------------------------------
+# returns the volume normalization factors:
+#   normalization used by zobov (assumes cubmic volume)
+#   normalization used in galaxy survey volume for observations
+def getVolNorm(sample):
+
+    sampleDir = sample.outputDir
+
+    infoFile = sampleDir+"/zobov_slice_"+sample.fullName+".par"
+    File = NetCDFFile(infoFile, 'r')
+    ranges = np.zeros((3,2))
+    ranges[0][0] = getattr(File, 'range_x_min')
+    ranges[0][1] = getattr(File, 'range_x_max')
+    ranges[1][0] = getattr(File, 'range_y_min')
+    ranges[1][1] = getattr(File, 'range_y_max')
+    ranges[2][0] = getattr(File, 'range_z_min')
+    ranges[2][1] = getattr(File, 'range_z_max')
+    isObservation = getattr(File, 'is_observation')
+    File.close()
+    mul = np.zeros((3))
+    mul[:] = ranges[:,1] - ranges[:,0]
+    
+    # getting the total number of tracers is an adventure depending
+    # on which verison of VIDE we're pulling up
+    maskIndexFile = sampleDir+"/mask_index.txt"
+    totalPartFile = sampleDir+"/total_particles.txt"
+
+    if os.path.exists(maskIndexFile):
+      nTot = float(open(totalPartFile, "r").read())
+      nGal = float(open(maskIndexFile, "r").read())
+    else:
+      nTot = float(open(totalPartFile, "r").read())
+      nGal = nTot
+
+    boxLen = mul
+
+    boxVol = np.prod(boxLen)
+    volNormZobov = nTot/boxVol
+    volNormObs = volNormZobov
+
+    if isObservation == 1:
+      if os.access(sample.maskFile, os.F_OK):
+        maskFile = sample.maskFile
+      else:
+        maskFile = sampleDir+"/"+os.path.basename(sample.maskFile)
+        print("Using maskfile found in: " + maskFile)
+
+      props = getSurveyProps(sample)
+      surveyVol = props[0]
+      volNormObs = nGal/surveyVol
+
+    return volNormZobov, volNormObs
+
+
 # -----------------------------------------------------------------------------
 # returns the nside resolution from the given maskfile
 def getNside(maskFile):

python_source/voidUtil/catalogUtil.py

@@ -126,58 +126,6 @@ def loadPart(sampleDir):
 
     return partData, boxLen, volNorm, isObservationData, ranges, extraData
 
-# -----------------------------------------------------------------------------
-def getVolNorm(sampleDir):
-    with open(sampleDir+"/sample_info.dat", 'rb') as input:
-      sample = pickle.load(input)
-
-    infoFile = sampleDir+"/zobov_slice_"+sample.fullName+".par"
-    File = NetCDFFile(infoFile, 'r')
-    ranges = np.zeros((3,2))
-    ranges[0][0] = getattr(File, 'range_x_min')
-    ranges[0][1] = getattr(File, 'range_x_max')
-    ranges[1][0] = getattr(File, 'range_y_min')
-    ranges[1][1] = getattr(File, 'range_y_max')
-    ranges[2][0] = getattr(File, 'range_z_min')
-    ranges[2][1] = getattr(File, 'range_z_max')
-    isObservation = getattr(File, 'is_observation')
-    File.close()
-    mul = np.zeros((3))
-    mul[:] = ranges[:,1] - ranges[:,0]
-
-    # getting the total number of tracers is an adventure depending
-    # on which verison of VIDE we're pulling up
-    maskIndexFile = sampleDir+"/mask_index.txt"
-    totalPartFile = sampleDir+"/total_particles.txt"
-
-    if os.path.exists(maskIndexFile):
-      nTot = float(open(totalPartFile, "r").read())
-      nGal = float(open(maskIndexFile, "r").read())
-    else:
-      nTot = float(open(totalPartFile, "r").read())
-      nGal = nTot
-
-    boxLen = mul
-
-    boxVol = np.prod(boxLen)
-    volNormZobov = nTot/boxVol
-    volNormObs = volNormZobov
-
-    if isObservation == 1:
-      if os.access(sample.maskFile, os.F_OK):
-        maskFile = sample.maskFile
-      else:
-        maskFile = sampleDir+"/"+os.path.basename(sample.maskFile)
-        print("Using maskfile found in: " + maskFile)
-
-
-      props = getSurveyProps(sample)
-      surveyVol = props[0]
-      volNormObs = nGal/surveyVol
-
-    return volNormZobov, volNormObs
-
-
 # -----------------------------------------------------------------------------
 def loadPartVel(sampleDir):
     #print "  Loading particle velocities..."
@@ -356,7 +304,7 @@ def loadVoidCatalog(sampleDir,
   catalog.ranges = ranges
   File.close()
 
-  volNormZobov, volNormObs = getVolNorm(sampleDir)
+  volNormZobov, volNormObs = getVolNorm(sample)
   catalog.volNormZobov = volNormZobov
   catalog.volNormObs = volNormObs