renamed start and end stage parameters; removed unused 'regenerate' flag

c_source/pruning/pruneVoids.cpp

@@ -188,7 +188,6 @@ int main(int argc, char **argv) {
  
   int i, p, p2, numPartTot, numZonesTot, dummy, iVoid;
   int numVoids;
-  double tolerance;
   FILE *fp;
   PART *part, *voidPart, *flaggedPart;
   ZONE2PART *zones2Parts;
@@ -212,7 +211,6 @@ int main(int argc, char **argv) {
   gsl_eigen_symmv_workspace *eigw = gsl_eigen_symmv_alloc(3);
 
   numVoids = args.numVoids_arg;
-  tolerance = args.tolerance_arg;
 
   clock1 = clock();
 
@@ -271,9 +269,6 @@ int main(int argc, char **argv) {
   // which is all particles (including mock boundary galaxies used in old
   // versions of VIDE) divided by the total volume of the bounding box
   volNorm = numPartTot/(boxLen[0]*boxLen[1]*boxLen[2]);
-  printf(" VOL NORM = %f\n", volNorm);
-
-  printf(" MAX CENTRAL DEN = %e\n", args.maxCentralDen_arg);
 
   fread(&dummy, 1, 4, fp);
   fread(temp, numPartTot, 4, fp);

c_source/pruning/pruneVoids.ggo

@@ -4,9 +4,9 @@ version "alpha"
 
 option "configFile" - "Configuration filename" string optional
 
-option "partFile" - "Particle file from generateFromCatalog" string required
+option "partFile" - "Particle file from prepObservation" string required
 
-option "extraInfo" - "Extra particle file from generateFromCatalog" string required
+option "extraInfo" - "Extra particle file from prepObservation" string required
 
 option "voidDesc" - "Void list from ZOBOV" string required
 
@@ -31,12 +31,11 @@ option "omegaM" - "Omega_M for redshift convertion" double optional default="0.2
 option "rMin" - "Minimum allowable void radius" double optional default="0.0"
 
 option "outputDir" - "Directory to place outputs" string required
+
 option "sampleName" - "unique string to assign to outputs" string required
 
 option "periodic" - "Set of edges which are periodic" string optional default="xy"
 
-option "tolerance" - "Fraction of void width to consider edge" double optional default="1.0"
-
 option "centralRadFrac" - "Fraction of void radii to consider central region" double optional default="4"
 
 option "maxCentralDen" - "Maximum central density to accept as a void" double optional default="0.2" 

examples/example_observation/example_observation.py

@@ -30,8 +30,8 @@ continueRun = False
 #   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
+startStage = 1
+endStage   = 3
 
 basePath = os.path.dirname(os.path.abspath(__file__))
 
@@ -55,7 +55,7 @@ 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
+#   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

examples/example_simulation/example_simulation.py

@@ -32,8 +32,8 @@ continueRun = False
 #   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
+startStage = 1
+endStage   = 3
 
 # directory for the input simulation files
 catalogDir = PWD

python_source/backend/launchers.py

@@ -52,18 +52,13 @@ class Bunch:
 # -----------------------------------------------------------------------------
 def launchPrep(sample, binPath, workDir=None, inputDataDir=None,
                outputDir=None, figDir=None, logFile=None, useComoving=False,
-               continueRun=None, regenerate=False):
+               continueRun=None):
 
   startTime = time.time()
 
   if sample.dataType == "observation":
     sampleName = sample.fullName
 
-    if regenerate:
-      inputParameterFlag = "inputParameter " + outputDir + \
-                           "/zobov_slice_"+sampleName+".par"
-      outputFile = outputDir + "/regenerated_zobov_slice_" + sampleName
-    else:
     inputParameterFlag = ""
     outputFile = outputDir + "/zobov_slice_" + sampleName
 
@@ -103,7 +98,7 @@ def launchPrep(sample, binPath, workDir=None, inputDataDir=None,
 
     parmFile = os.getcwd()+"/prep_"+sample.fullName+".par"
 
-    if regenerate or not (continueRun and jobSuccessful(logFile, "Done!\n")):
+    if not (continueRun and jobSuccessful(logFile, "Done!\n")):
       with open(parmFile, mode="wt") as f:
         f.write(conf)
 
@@ -453,8 +448,6 @@ def launchZobov(sample, binPath, outputDir=None, logDir=None, continueRun=None,
                                      kind='cubic', bounds_error=False,
                                      fill_value=1.0)
       # re-weight and write
-       ## TEST
-      #redshifts /= 10000.
       for i in range(len(vols)):
         vols[i] *= selfunc(redshifts[i])
 
@@ -573,8 +566,7 @@ def launchZobov(sample, binPath, outputDir=None, logDir=None, continueRun=None,
 # -----------------------------------------------------------------------------
 def launchPrune(sample, binPath,
                 summaryFile=None, logFile=None, outputDir=None,
-                continueRun=None, useComoving=False, mergingThreshold=0.2,
-                boundaryTolerance=1.0):
+                continueRun=None, useComoving=False, mergingThreshold=0.2):
 
   startTime = time.time()
 
@@ -626,7 +618,6 @@ def launchPrune(sample, binPath,
     cmd += " --partAdj=" + outputDir+"/adj_"+str(sampleName)+".dat"
     cmd += " --partEdge=" + outputDir+"galaxy_edge_flags.txt"
     cmd += " --extraInfo=" + outputDir+"/zobov_slice_"+str(sampleName)+".par"
-    cmd += " --tolerance=" + str(boundaryTolerance)
     cmd += " --maxCentralDen=" + str(maxDen)
     cmd += " --rMin=" + str(minRadius)
     cmd += " --numVoids=" + str(numVoids)
@@ -638,7 +629,6 @@ def launchPrune(sample, binPath,
     cmd += " --outputDir=" + outputDir
     cmd += " --sampleName=" + str(sampleName)
     log = open(logFile, 'w')
-    #log.write(f"Command is {cmd}\n")
     subprocess.call(cmd, stdout=log, stderr=log, shell=True)
     log.close()
 

python_source/vide_pipeline/__main__.py

@@ -43,12 +43,10 @@ if (len(sys.argv) > 1):
     print("  Cannot find parameter file %s!" % filename)
     exit(-1)
   parms = imp.load_source("name", filename)
-  regenerateFlag = False
   globals().update(vars(parms))
   void_path = os.path.split(voidUtil.__file__)[0]
   ZOBOV_PATH=f'{void_path}/../vide/bin/' # this needs to be cleaned up
   CTOOLS_PATH=ZOBOV_PATH
-  #print(f"ZOBOV_PATH is  {ZOBOV_PATH}")
 else:
   print(" Using default parameters")
 
@@ -64,11 +62,11 @@ if not os.access(figDir, os.F_OK):
 if not continueRun:
   print(" Cleaning out log files...")
 
-  if startCatalogStage <= 1 and glob.glob(logDir+"/prepare*") != []:
+  if startStage <= 1 and glob.glob(logDir+"/prepare*") != []:
     os.system("rm %s/prepare*" % logDir)
-  if startCatalogStage <= 2 and glob.glob(logDir+"/zobov*") != []:
+  if startStage <= 2 and glob.glob(logDir+"/zobov*") != []:
     os.system("rm %s/zobov*" % logDir)
-  if startCatalogStage <= 3 and glob.glob(logDir+"/prune*") != []:
+  if startStage <= 3 and glob.glob(logDir+"/prune*") != []:
     os.system("rm %s/prune*" % logDir)
 
 for sample in dataSampleList:
@@ -83,7 +81,7 @@ for sample in dataSampleList:
     os.makedirs(outputDir)
 
 # ---------------------------------------------------------------------------
-  if (startCatalogStage <= 1) and (endCatalogStage >= 1) and not sample.isCombo:
+  if (startStage <= 1) and (endStage >= 1) and not sample.isCombo:
     print("  Preparing tracers from catalog...", end='')
     sys.stdout.flush()
 
@@ -97,10 +95,10 @@ for sample in dataSampleList:
     launchPrep(sample, PREPARE_PATH, workDir=workDir, 
                inputDataDir=inputDataDir, outputDir=outputDir,
                figDir=figDir, logFile=logFile, useComoving=sample.useComoving,
-               continueRun=continueRun, regenerate=regenerateFlag)
+               continueRun=continueRun)
 
   # --------------------------------------------------------------------------
-  if (startCatalogStage <= 2) and (endCatalogStage >= 2) and not sample.isCombo:
+  if (startStage <= 2) and (endStage >= 2) and not sample.isCombo:
     print("  Finding voids...", end='')
     sys.stdout.flush()
 
@@ -110,7 +108,7 @@ for sample in dataSampleList:
                  mergingThreshold=mergingThreshold)
 
   # -------------------------------------------------------------------------
-  if (startCatalogStage <= 3) and (endCatalogStage >= 3) and not sample.isCombo:
+  if (startStage <= 3) and (endStage >= 3) and not sample.isCombo:
 
     print("  Pruning void catalogs...", end='')
     sys.stdout.flush()
@@ -124,20 +122,4 @@ for sample in dataSampleList:
                 useComoving=sample.useComoving, continueRun=continueRun,
                 mergingThreshold=mergingThreshold)
 
-# -------------------------------------------------------------------------
-if (startCatalogStage <= 4) and (endCatalogStage >= 4):
-
-  print("  Plotting...", end='')
-  sys.stdout.flush()
-
-  #for thisDataPortion in dataPortions:
-    #plotRedshiftDistribution(workDir, dataSampleList, figDir, showPlot=False, 
-    #                         dataPortion=thisDataPortion, setName=setName)
-    #plotSizeDistribution(workDir, dataSampleList, figDir, showPlot=False, 
-    #                         dataPortion=thisDataPortion, setName=setName)
-    #plotNumberDistribution(workDir, dataSampleList, figDir, showPlot=False, 
-    #                         dataPortion=thisDataPortion, setName=setName)
-    #plotVoidDistribution(workDir, dataSampleList, figDir, showPlot=False, 
-    #                         dataPortion=thisDataPortion, setName=setName)
-
 print("\n VIDE finished!")

python_source/vide_pipeline/vide_prepare_simulation.py

@@ -165,14 +165,14 @@ import os
 from backend.classes import *
 
 continueRun = {continueRun} # set to True to enable restarting aborted jobs
-startCatalogStage = {startCatalogStage}
-endCatalogStage   = {endCatalogStage}
+startStage = {startStage}
+endStage   = {endStage}
 
 dataSampleList = []
            """
 
-  scriptFile.write(header.format(startCatalogStage=startCatalogStage,
-                                 endCatalogStage=endCatalogStage,
+  scriptFile.write(header.format(startStage=startStage,
+                                 endStage=endStage,
                                  continueRun=continueRun,
                                 ))