size of subdivison buffer now a parameter

examples/example_observation/example_observation.py

@@ -46,20 +46,19 @@ logDir = os.path.join(workDir,"logs","example_observation")
 
 # output directory for figures
 # optimization: maximum number of parallel threads to use
-numZobovThreads = 8
+numZobovThreads = 1
 
 # optimization: number of subdivisions of the volume
 numZobovDivisions = 2
 
+# buffer size (in fraction of the boz size) when sub-diving volumes
+zobovBuffer = 0.1
+
 # Maximum density for merging voids
 #   0 (equivalent to infinitely large value) -> Merge everything (no threshold)
 #   1e-9 (or smaller, but != 0) -> Do not merge anything
 mergingThreshold = 1e-9
 
-# 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/vide_pipeline/defaults.py

@@ -37,9 +37,6 @@ endCatalogStage = 3
 # if True, will scan log files for last known completed state and run from there
 continueRun = True
 
-# re-build the inputs?
-regenerateFlag = False
-
 # directory for the input simulation/observational particle files
 catalogDir = os.getenv("HOME")+"/workspace/Voids/catalog/"
 
@@ -132,11 +129,13 @@ haloFileColSep = ','
 haloFileNumComLines = 0
 haloFilePosRescale = 1.0 # rescaling necessary to get Mpc/h
 
-# adjust these two parameters given the memory contraints on your system:
+# adjust these parameters given the memory contraints on your system:
 #   numZobovDivisions: how many sub-volumes per dimension will zobov process
 #   numZobovThreads: how many sub-volumes to process at once?   
+#   zobovBuffer: fraction of the domain to add to each sub-division
 numZobovDivisions = 2
 numZobovThreads = 2
+zobovBuffer = 0.1
 
 # Maximum density for merging voids
 #   0 (equivalent to infinitely large value) -> Merge everything (no threshold)