allowed high-z threshold for cutting to be user-selectable

examples/example_observation/example_observation.py

@@ -34,14 +34,12 @@ startCatalogStage = 1
 endCatalogStage   = 3
 
 basePath = os.path.dirname(os.path.abspath(__file__))
-#basePath = os.path.abspath(os.path.join(basePath,"..","..","..","examples"))
 
 # directory for input data files
 inputDataDir = basePath
 
 # void catalog output directory
 workDir = basePath
-#workDir = os.path.join(basePath,"example_observation")
 
 # output directory for log files
 logDir = os.path.join(workDir,"logs","example_observation")
@@ -60,6 +58,13 @@ numZobovDivisions = 2
 #   1e-9 (or smaller != 0) -> Do not merge anything
 mergingThreshold = 1e-9
 
+# for observations, when cutting voids at the high-z boundary, what multiple
+#   of the radius to cut
+#   0: all voids with centers less than z_max will be allowed
+#   1: all voids at least 1*radius away from z_max will be allowed
+#   Any other nummber: aall voids at least tolerance*radius will be allowed
+highRedshiftTolerance = 1.0
+
 # don't change this
 dataSampleList = []
 
@@ -98,7 +103,7 @@ newSample = Sample(
 
                    # density of mock particles in cubic Mpc/h
                    # (make this as high as you can afford)
-                   fakeDensity = 0.05,
+                   fakeDensity = 0.0000001,
 
                    # if true, convert to comoving space using LCDM cosmology
                    useComoving = True,

python_source/backend/launchers.py

@@ -467,7 +467,8 @@ def launchZobov(sample, binPath, zobovDir=None, logDir=None, continueRun=None,
 # -----------------------------------------------------------------------------
 def launchPrune(sample, binPath,
                 summaryFile=None, logFile=None, zobovDir=None,
-                continueRun=None, useComoving=False, mergingThreshold=0.2):
+                continueRun=None, useComoving=False, mergingThreshold=0.2,
+                highRedshiftTolerance=1.0):
 
   sampleName = sample.fullName
 
@@ -516,7 +517,7 @@ def launchPrune(sample, binPath,
     cmd += " --partAdj=" + zobovDir+"/adj_"+str(sampleName)+".dat"
     cmd += " --extraInfo=" + zobovDir+"/zobov_slice_"+str(sampleName)+\
            ".par"
-    cmd += " --tolerance=1.0"
+    cmd += " --tolerance=" + str(highRedshiftTolerance)
     cmd += " --mockIndex=" + str(mockIndex)
     cmd += " --maxCentralDen=" + str(maxDen)
     cmd += " --zMin=" + str(sample.zRange[0])

python_source/vide_pipeline/__main__.py

@@ -121,7 +121,8 @@ for sample in dataSampleList:
     launchPrune(sample, PRUNE_PATH, 
                 logFile=logFile, zobovDir=zobovDir, 
                 useComoving=sample.useComoving, continueRun=continueRun,
-                mergingThreshold=mergingThreshold)
+                mergingThreshold=mergingThreshold,
+                highRedshiftTolerance=highRedshiftTolerance)
 
 # -------------------------------------------------------------------------
 if (startCatalogStage <= 4) and (endCatalogStage >= 4):

python_source/vide_pipeline/defaults.py

@@ -143,6 +143,13 @@ numZobovThreads = 2
 #   1e-9 (or smaller != 0) -> Do not merge anything
 mergingThreshold = 1.e-9
 
+# for observations, when cutting voids at the high-z boundary, what multiple
+#   of the radius to cut
+#   0: all voids with centers less than z_max will be allowed
+#   1: all voids at least 1*radius away from z_max will be allowed
+#   Any other nummber: aall voids at least tolerance*radius will be allowed
+highRedshiftTolerance = 1.0
+
 # simulation information
 numPart = 512*512*512
 lbox = 999.983 # Mpc/h