FIXED zobov bug when only using one subdomain; added zobov buffer as tunable parameter

python_source/backend/launchers.py

@@ -353,6 +353,7 @@ def launchPrep(sample, binPath, workDir=None, inputDataDir=None,
 # -----------------------------------------------------------------------------
 def launchZobov(sample, binPath, outputDir=None, logDir=None, continueRun=None,
                  numZobovDivisions=None, numZobovThreads=None, 
+                 zobovBuffer=0.1,
                  mergingThreshold=0.2):
 
   startTime = time.time()
@@ -382,9 +383,14 @@ def launchZobov(sample, binPath, outputDir=None, logDir=None, continueRun=None,
     if os.access(outputDir+"/voidDesc_"+sampleName+".out", os.F_OK):
       os.unlink(outputDir+"/voidDesc_"+sampleName+".out")
 
-    cmd = [binPath+"/vozinit", datafile, "0.1", "1.0", str(numZobovDivisions), \
+    isObs = 0
+    if sample.dataType == "observation":
+      isObs = 1
+
+    cmd = [binPath+"/vozinit", datafile, str(zobovBuffer), \
+                      "1.0", str(numZobovDivisions), \
                       "_"+sampleName, str(numZobovThreads), \
-                      binPath, outputDir]
+                      binPath, outputDir, str(isObs)]
     log = open(logFile, 'w')
     subprocess.call(cmd, stdout=log, stderr=log)
     log.close()

python_source/vide_pipeline/__main__.py

@@ -101,6 +101,7 @@ for sample in dataSampleList:
     launchZobov(sample, ZOBOV_PATH, outputDir=outputDir, logDir=logDir, 
                 continueRun=continueRun, numZobovDivisions=numZobovDivisions,
                  numZobovThreads=numZobovThreads,
+                 zobovBuffer=zobovBuffer,
                  mergingThreshold=mergingThreshold)
 
   # -------------------------------------------------------------------------

python_source/voidUtil/catalogUtil.py

@@ -258,9 +258,7 @@ def loadVoidCatalog(sampleDir,
 #   clearNearBoundaries: remove voids where the maximum extent is
 #                        greater than the distance to nearest edge
 #   maxHighCentralDen: if != -1, filters based on based on central density
-
-# NOTE: we are moving away from the cumbersome void catalog outputs of
-#       older versions, and will eventually just output a single catalog.
+#
 #       To replicate the old "central" catalog, choose:
 #         clearEdges = True
 #         clearTree = True