renamed tolerance parameter to better reflect its function

examples/example_observation/example_observation.py

@@ -58,12 +58,9 @@ 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
+# when trimming away voids near the bounaries, what multiple of the radius to
+#   use for safety
+boundaryTolerance = 1.0
 
 # don't change this
 dataSampleList = []

python_source/backend/launchers.py

@@ -468,7 +468,7 @@ 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,
-                highRedshiftTolerance=1.0):
+                boundaryTolerance=1.0):
 
   sampleName = sample.fullName
 
@@ -517,7 +517,7 @@ def launchPrune(sample, binPath,
     cmd += " --partAdj=" + zobovDir+"/adj_"+str(sampleName)+".dat"
     cmd += " --extraInfo=" + zobovDir+"/zobov_slice_"+str(sampleName)+\
            ".par"
-    cmd += " --tolerance=" + str(highRedshiftTolerance)
+    cmd += " --tolerance=" + str(boundaryTolerance)
     cmd += " --mockIndex=" + str(mockIndex)
     cmd += " --maxCentralDen=" + str(maxDen)
     cmd += " --zMin=" + str(sample.zRange[0])

python_source/vide_pipeline/__main__.py

@@ -122,7 +122,7 @@ for sample in dataSampleList:
                 logFile=logFile, zobovDir=zobovDir, 
                 useComoving=sample.useComoving, continueRun=continueRun,
                 mergingThreshold=mergingThreshold,
-                highRedshiftTolerance=highRedshiftTolerance)
+                boundaryTolerance=boundaryTolerance)
 
 # -------------------------------------------------------------------------
 if (startCatalogStage <= 4) and (endCatalogStage >= 4):

python_source/vide_pipeline/defaults.py

@@ -143,12 +143,9 @@ 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
+# when trimming away voids near the bounaries, what multiple of the radius to
+#   use for safety
+boundaryTolerance = 1.0
 
 # simulation information
 numPart = 512*512*512