eliminated extranneous/deprecated parameters: zRange (for filtering voids on redshift range during pruning) and fakeDensity (for inserting boundary particles)

c_source/prep/prepObservation.ggo

@@ -5,7 +5,6 @@ option "configFile" - "Configuration filename" string optional
 
 option "catalog" - "Input NYU-VAGC catalog" string required
 option "mask" - "Healpix mask of unobserved data (in Equatorial coordinates)" string required
-option "density_fake" - "Number density of boundary fake tracers (1 h^3/ Mpc^3)"  double optional default="1"
 
 option "zMin" - "Minimum redshift of data" double required
 

c_source/pruning/pruneVoids.cpp

@@ -215,10 +215,6 @@ int main(int argc, char **argv) {
   tolerance = args.tolerance_arg;
 
   clock1 = clock();
-  printf("Pruning parameters: %f %f %f %s\n", args.zMin_arg, 
-                                             args.zMax_arg,
-                                             args.rMin_arg,
-                                             args.periodic_arg);
 
   // check for periodic box
   periodicX = 0;
@@ -747,20 +743,6 @@ int main(int argc, char **argv) {
                             pow(voids[iVoid].macrocenter[2] - boxLen[2]/2.,2));
       //voids[iVoid].redshiftInMpc = voids[iVoid].redshiftInMpc;
 
-
-      if (args.useComoving_flag) {
-        redshift = gsl_interp_eval(interp, dL, redshifts,
-                                   voids[iVoid].redshiftInMpc, acc);
-        nearestEdge = fabs((redshift-args.zMax_arg)*LIGHT_SPEED/100.); 
-        voids[iVoid].redshift = redshift;
-      } else {
-        redshift = voids[iVoid].redshiftInMpc;
-        nearestEdge = fabs(redshift-args.zMax_arg*LIGHT_SPEED/100.); 
-        voids[iVoid].redshift = voids[iVoid].redshiftInMpc/LIGHT_SPEED*100.;
-      }
-      //nearestEdge = fmin(fabs(redshift-args.zMin_arg*LIGHT_SPEED/100.), 
-      //                   fabs(redshift-args.zMax_arg*LIGHT_SPEED/100.)); 
-
     } else {
 
       voids[iVoid].redshiftInMpc = voids[iVoid].macrocenter[2];
@@ -901,48 +883,6 @@ int main(int argc, char **argv) {
   voids.resize(iGood);
   printf("  2nd filter: rejected %d too small\n", numTooSmall); 
 
-/*
-  // toss out voids near non-periodic box edges
-  iGood = 0;
-  for (iVoid = 0; iVoid < voids.size(); iVoid++) {
-    if (voids[iVoid].maxRadius > voids[iVoid].nearestEdge || 
-        voids[iVoid].radius > voids[iVoid].nearestEdge) {
-      numNearZ++;
-    } else {
-      voids[iGood++] = voids[iVoid];
-    }
-  }
-  voids.resize(iGood);
-  printf("  3rd filter: rejected %d too close to high redshift boundaries\n", numNearZ); 
-*/
-
-/*
-  // toss out voids that are beyond redshift boundaries
-  numNearZ = 0;
-  iGood = 0;
-  for (iVoid = 0; iVoid < voids.size(); iVoid++) {
-    // assume the lower z-boundary is "soft" in observations
-    if (args.isObservation_flag && 
-        voids[iVoid].redshift < args.zMin_arg) {
-      numNearZ++;
-     } else {
-      voids[iGood++] = voids[iVoid];
-    }
-  }
-  voids.resize(iGood);
-
-  iGood = 0;
-  for (iVoid = 0; iVoid < voids.size(); iVoid++) {
-    if (args.isObservation_flag && voids[iVoid].redshift > args.zMax_arg) {
-      numNearZ++;
-     } else {
-      voids[iGood++] = voids[iVoid];
-    }
-  }
-  voids.resize(iGood);
-  printf("  4th filter: rejected %d outside redshift boundaries\n", numNearZ); 
-*/
-
   // find top-level voids
   numAreParents = 0;
   iGood = 0;

c_source/pruning/pruneVoids.ggo

@@ -28,9 +28,6 @@ option "useComoving" - "Void positions are in comoving coordinates" flag off
 
 option "omegaM" - "Omega_M for redshift convertion" double optional default="0.27"
 
-option "zMin" - "Minimum redshift of sample" double optional default="0.0"
-option "zMax" - "Maximum redshift of sample" double optional default="10.0"
-
 option "rMin" - "Minimum allowable void radius" double optional default="0.0"
 
 option "outputDir" - "Directory to place outputs" string required

examples/example_observation/example_observation.py

@@ -48,10 +48,10 @@ logDir = os.path.join(workDir,"logs","example_observation")
 figDir = os.path.join(workDir,"figs","example_observation")
 
 # optimization: maximum number of parallel threads to use
-numZobovThreads = 2
+numZobovThreads = 8
 
 # optimization: number of subdivisions of the volume
-numZobovDivisions = 1
+numZobovDivisions = 2
 
 # Maximum density for merging voids
 #   0 (equivalent to infinitely large value) -> Merge everything (no threshold)
@@ -91,6 +91,7 @@ newSample = Sample(
                    # resolution for HEALpix mapping of survey edge contours
                    #   Set to -1 to use nside from given fits file
                    #   MUST be set if auto-computing mask
+                   #nsideForContour = -1,
                    nsideForContour = 128,
 
                    # radial selection function (if not volume limited)
@@ -99,9 +100,6 @@ newSample = Sample(
                    # max and min redshifts of galaxies in your sample
                    zBoundary = (0.0, 0.15),
 
-                   # max and min redshifts where you want to find voids
-                   zRange = (0.1, 0.15),
-
                    # width of redshift boundaries to flag edge galaxies
                    # (interpreted as boundaryWidth*(zMax-zMin))
                    boundaryWidth = 0.01,
@@ -110,11 +108,6 @@ newSample = Sample(
                    # or specify your own in Mpc/h
                    minVoidRadius = -1,
 
-                   # density of mock particles in cubic Mpc/h
-                   # (make this as high as you can afford)
-                   ### DEPRECATED
-                   fakeDensity = 0.05,
-
                    # if true, convert to comoving space using LCDM cosmology
                    useComoving = True,
 

python_source/backend/classes.py

@@ -71,16 +71,14 @@ class Sample:
   outputDir = ""
   maskFile = "rast_window_512.fits"
   nsideForContour = 128
-  selFunFile = "czselfunc.all.dr72dim.dat"
+  selFunFile = None
   zBoundary = (0.0, 0.1)
   zBoundaryMpc = (0., 300)
   boundaryWidth = 0.02
   shiftSimZ = False
-  zRange    = (0.0, 0.1)
   omegaM    = 0.27
   minVoidRadius = -1
   meanPartSep = 1 # calculated mean particle separation
-  fakeDensity = 0.01 # TODO - remove
   hasWeightedVolumes = False
   profileBinSize = 2 # Mpc
   autoNumInStack = -1 # set to >0 to automatically generate stacks of size N
@@ -104,9 +102,9 @@ class Sample:
 
   def __init__(self, dataFile="", fullName="", dataUnit=1,
                nickName="", maskFile="", nsideForContour=128, selFunFile="",
-               zBoundary=(), zRange=(), zBoundaryMpc=(), boundaryWidth=0.1,
+               zBoundary=(), zBoundaryMpc=(), boundaryWidth=0.1,
                shiftSimZ=False, meanPartSep = 1,
-               minVoidRadius=-1, fakeDensity=0.01, volumeLimited=True,
+               minVoidRadius=-1, volumeLimited=True,
                numAPSlices=1, hasWeightedVolumes=False,
                includeInHubble=True, partOfCombo=False, isCombo=False, 
                comboList=(), profileBinSize=2.0,
@@ -126,10 +124,8 @@ class Sample:
     self.zBoundaryMpc = zBoundaryMpc
     self.boundaryWidth = boundaryWidth
     self.shiftSimZ = shiftSimZ
-    self.zRange = zRange
     self.minVoidRadius = minVoidRadius
     self.meanPartSep = meanPartSep
-    self.fakeDensity = fakeDensity
     self.hasWeightedVolumes = hasWeightedVolumes
     self.volumeLimited = volumeLimited
     self.includeInHubble = includeInHubble 

python_source/backend/launchers.py

@@ -91,14 +91,13 @@ def launchPrep(sample, binPath, workDir=None, inputDataDir=None,
       params %s
       zMin %g
       zMax %g
-      density_fake %g
       %s
       %s
       omegaM %g
       nsideForContour %g
       """ % (datafile, sample.maskFile, outputFile,
              outputDir+"/zobov_slice_"+sampleName+".par",
-             sample.zBoundary[0], sample.zBoundary[1], sample.fakeDensity,
+             sample.zBoundary[0], sample.zBoundary[1],
              useComovingFlag, inputParameterFlag, sample.omegaM,
              sample.nsideForContour)
 
@@ -629,8 +628,6 @@ def launchPrune(sample, binPath,
     cmd += " --extraInfo=" + outputDir+"/zobov_slice_"+str(sampleName)+".par"
     cmd += " --tolerance=" + str(boundaryTolerance)
     cmd += " --maxCentralDen=" + str(maxDen)
-    cmd += " --zMin=" + str(sample.zRange[0])
-    cmd += " --zMax=" + str(sample.zRange[1])
     cmd += " --rMin=" + str(minRadius)
     cmd += " --numVoids=" + str(numVoids)
     cmd += observationLine

python_source/vide_pipeline/vide_prepare_simulation.py

@@ -204,7 +204,6 @@ newSample = Sample(dataFile = "{dataFile}",
                    nickName = "{nickName}",
                    dataType = "simulation",
                    zBoundary = ({zMin}, {zMax}),
-                   zRange    = ({zMin}, {zMax}),
                    zBoundaryMpc = ({zMinMpc}, {zMaxMpc}),
                    shiftSimZ = {shiftSimZ},
                    omegaM    = {omegaM},