placed mergingThreshold parameter in defaults file

examples/example_observation/example_observation.py

@@ -44,10 +44,10 @@ workDir = basePath
 #workDir = os.path.join(basePath,"example_observation")
 
 # output directory for log files
-logDir = os.path.join(basePath,"logs","example_observation")
+logDir = os.path.join(workDir,"logs","example_observation")
 
 # output directory for figures
-figDir = os.path.join(basePath,"figs","example_observation")
+figDir = os.path.join(workDir,"figs","example_observation")
 
 # optimization: maximum number of parallel threads to use
 numZobovThreads = 2

examples/example_simulation/example_simulation.py

@@ -74,7 +74,7 @@ numZobovDivisions = 2
 # maximum density for merging voids
 #   0 (equivalent to infinitely large value) -> Merge everything (no threshold)
 #   1e-9 (or smaller != 0) -> Do not merge anything
-mergingThreshold = 1e-9
+mergingThreshold = 0.2
 
 # prefix to give all outputs
 prefix = "sim_"

python_source/backend/launchers.py

@@ -323,7 +323,8 @@ def launchPrep(sample, binPath, workDir=None, inputDataDir=None,
 
 # -----------------------------------------------------------------------------
 def launchZobov(sample, binPath, zobovDir=None, logDir=None, continueRun=None,
-                 numZobovDivisions=None, numZobovThreads=None, mergingThreshold=0.2):
+                 numZobovDivisions=None, numZobovThreads=None, 
+                 mergingThreshold=0.2):
 
   sampleName = sample.fullName
 

python_source/vide_pipeline/defaults.py

@@ -23,12 +23,23 @@ import os
 # -----------------------------------------------------------------------------
 # DEFAULT CONFIGURATION
 
+# the overall name for your dataset
 datasetName = ""
 
+# where to start and end the VIDE pipeline
+# stages:
+#   1 : extract redshift slices from data
+#   2 : void extraction using zobov
+#   3 : removal of small voids and voids near the edge
 startCatalogStage = 1
 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/"
 
@@ -36,9 +47,9 @@ catalogDir = os.getenv("HOME")+"/workspace/Voids/catalog/"
 hodPath = os.getenv("HOME")+"/projects/Voids/hod/HOD.x"
 
 # where to put the final void catalog, figures, and output logs
-voidOutputDir = os.getenv("HOME")+"/workspace/Voids//"
-figDir = os.getenv("PWD")+"/../figs/"
-logDir = os.getenv("PWD")+"/../logs/"
+workDir = os.getenv("PWD")+"/output/"
+figDir = os.getenv("PWD")+"/figs/"
+logDir = os.getenv("PWD")+"/logs/"
 
 # where to place the pipeline scripts
 scriptDir = os.getenv("PWD")+"/scripts//"
@@ -127,6 +138,11 @@ haloFilePosRescale = 1.0 # rescaling necessary to get Mpc/h
 numZobovDivisions = 2
 numZobovThreads = 2
 
+# Maximum density for merging voids
+#   0 (equivalent to infinitely large value) -> Merge everything (no threshold)
+#   1e-9 (or smaller != 0) -> Do not merge anything
+mergingThreshold = 1.e-9
+
 # simulation information
 numPart = 512*512*512
 lbox = 999.983 # Mpc/h

python_source/vide_pipeline/vide_prepare_simulation.py

@@ -53,7 +53,7 @@ parser.add_argument('--parm', dest='parm',
 args = parser.parse_args()
 
 
-defaultsFile = "@CMAKE_SOURCE_DIR@/python_source/pipeline/defaults.py"
+defaultsFile = "@CMAKE_SOURCE_DIR@/python_source/vide_pipeline/defaults.py"
 parms = imp.load_source("name", defaultsFile)
 globals().update(vars(parms))
 
@@ -148,7 +148,7 @@ def getNickName(setName, sampleName):
 
 
 #------------------------------------------------------------------------------
-# for given dataset parameters, outputs a script for use with analyzeVoids
+# for given dataset parameters, outputs a script for use with VIDE pipeline
 def writeScript(setName, dataFileNameBase, dataFormat,
                 scriptDir, catalogDir, fileNums, redshifts, numSubvolumes,
                 numSlices, useVel, lbox, minRadius, omegaM, subsample=1.0, 
@@ -168,10 +168,6 @@ continueRun = {continueRun} # set to True to enable restarting aborted jobs
 startCatalogStage = {startCatalogStage}
 endCatalogStage   = {endCatalogStage}
 
-regenerateFlag = False
-
-mergingThreshold = 1e-9
-
 dataSampleList = []
            """
 
@@ -190,12 +186,14 @@ logDir = "{logDir}/{setName}/"
 
 numZobovDivisions = {numZobovDivisions}
 numZobovThreads = {numZobovThreads}
+mergingThreshold = {mergingThreshold}
                """
   scriptFile.write(dataInfo.format(setName=setName, figDir=figDir,
                                    logDir=logDir, voidOutputDir=voidOutputDir,
                                    inputDataDir=catalogDir, 
                                    numZobovDivisions=numZobovDivisions,
-                                   numZobovThreads=numZobovThreads))
+                                   numZobovThreads=numZobovThreads,
+                                   mergingThreshold=mergingThreshold))
 
 
   sampleInfo = """