Tesllation seems stable with new boundary handling procedure. Rooted out strange adjacency record-keeping due to some galaxies connecting to guard particles. Zobov still generates warning about guard particle encounters, but this is fine for observational datasets because we don't trust the tesselation at the edge galaxies anyway.

c_source/jozov2/jozov2_io.cpp

@@ -90,9 +90,10 @@ void readAdjacencyFile(const string& adjfile, PARTICLE*& p, pid_t& np)
                   }
                 else{
                 p[i].adj[p[i].ncnt] = j;
-                p[j].adj[p[j].ncnt] = i;
                 p[i].ncnt++; 
-                p[j].ncnt++; }
+                p[j].adj[p[j].ncnt] = i;
+                p[j].ncnt++; 
+                }
               }
             else
               {

c_source/prep/prepObservation.cpp

@@ -202,6 +202,44 @@ void placeGalaxiesInCube(NYU_VData& data, ParticleData& output_data,
     % (1e-2*output_data.box[1][1]) % (1e-2*output_data.box[1][0])
     % (1e-2*output_data.box[2][1]) % (1e-2*output_data.box[2][0]) << endl;
  
+
+/*
+// TEST DEBUG
+int nNewPerSide = 100;
+Position p;
+int idx = data.size() + 1;
+float xwidth = output_data.box[0][0] - output_data.box[0][1];
+float ywidth = output_data.box[1][0] - output_data.box[1][1];
+float zwidth = output_data.box[2][0] - output_data.box[2][1];
+
+float dx = xwidth / nNewPerSide;
+float dy = ywidth / nNewPerSide;
+float dz = zwidth / nNewPerSide;
+
+for (int i = 0; i < nNewPerSide; i++) {
+for (int j = 0; j < nNewPerSide; j++) {
+for (int k = 0; k < nNewPerSide; k++) {
+  p.xyz[0] = output_data.box[0][1] + i*dx;
+  p.xyz[1] = output_data.box[1][1] + j*dy;
+  p.xyz[2] = output_data.box[2][1] + k*dz;
+
+  cout << "INSERT " <<  p.xyz[0] << ", " << p.xyz[1] << ", " << p.xyz[2] << endl;
+  cout << "COMPARING " << output_data.pos[i].xyz[0] << endl;
+  output_data.pos.push_back(p);
+  output_data.id_gal.push_back(idx);
+  output_data.ra.push_back(-1);
+  output_data.dec.push_back(-1);
+  output_data.redshift.push_back(-1);
+  output_data.uniqueID.push_back(-1);
+
+  idx++;
+}
+}
+}
+*/
+// END TEST DEBUG
+
+
 }
 
 void flagEdgeGalaxies(prepObservation_info& args ,
@@ -230,8 +268,10 @@ void flagEdgeGalaxies(prepObservation_info& args ,
 
   // write a small text file with galaxy position (for diagnostic purposes)
   // TODO - remove this
+
   FILE *fp;
   fp = fopen("galaxies.txt", "w");
+  //for (int i = 0; i < output_data.id_gal.size(); i++) {  
   for (int i = 0; i < data.size(); i++) {  
     Position& p = output_data.pos[i];
     fprintf(fp, "%e %e %e\n", 
@@ -326,7 +366,7 @@ void saveForZobov(ParticleData& pdata, const string& fname,
   f.writeInt32(pdata.pos.size());
   f.endCheckpoint();
 
-
+  cout << format("Saving %d galaxies...") % pdata.pos.size() << endl;
   for (int j = 0; j < 3; j++)
     {
       cout << format("Writing %c components...") % axis[j] << endl;

c_source/zobov/jozov.c

@@ -162,7 +162,7 @@ int main(int argc,char **argv) {
       /*if (p[i].ncnt != p[i].nadj) {*/
     // END PMS
       p[i].nadj = p[i].ncnt;
-      printf("We didn't get all of %d's adj's; %d != %d.\n",i,nin,p[i].nadj);
+      printf("jovoz: We didn't get all of %d's adj's; %d != %d.\n",i,nin,p[i].nadj);
       /*exit(0);*/
     }
   }

c_source/zobov/voz1b1.c

@@ -138,7 +138,7 @@ int main(int argc, char *argv[]) {
     if (isitinbuf) nvpbuf++;
     if (isitinmain) nvp++;
   }
-  
+
   nvpbuf += 6*(NGUARD+1)*(NGUARD+1); /* number of guard
 					points */
 
@@ -305,8 +305,16 @@ int main(int argc, char *argv[]) {
     
     exitcode = vorvol(deladjs, points, intpoints, adjs[i].nadj, &(vols[i]));
     vols[i] *= (float)np;
-    if (i % 1000 == 0)
+    //if (i % 1000 == 0)
-      printf("%d: %d, %f\n",i,adjs[i].nadj,vols[i]);
+    //  printf("%d: %d, %f\n",i,adjs[i].nadj,vols[i]);
+  }
+
+// PMS - reset number of adjancies to not include links to border guards
+  for (i=0; i<nvp; i++) {
+    int nActual = 0;
+    for (j = 0; j < adjs[i].nadj; j++)
+      if (adjs[i].adj[j] < nvp) nActual++;
+    adjs[i].nadj = nActual;
   }
 
   /* Get the adjacencies back to their original values */
@@ -314,7 +322,7 @@ int main(int argc, char *argv[]) {
   for (i=0; i<nvp; i++)
     for (j = 0; j < adjs[i].nadj; j++)
       adjs[i].adj[j] = orig[adjs[i].adj[j]];
-  
+
   totalvol = 0.;
   for (i=0;i<nvp; i++) {
     totalvol += (double)vols[i];

python_source/backend/classes.py

@@ -21,8 +21,8 @@
 
 import os
 from numpy import abs
-import matplotlib as mpl
+#import matplotlib as mpl
-mpl.use('Agg')
+#mpl.use('Agg')
 
 LIGHT_SPEED = 299792.458
 

python_source/backend/launchers.py

@@ -118,6 +118,7 @@ def launchPrep(sample, binPath, workDir=None, inputDataDir=None,
 
         # flag edge galaxies with python routine for now
         galFile = outputDir+"/zobov_slice_"+sampleName
+        os.system("mv %s %s" % ("galaxies.txt", outputDir))
         #galFile = outputDir + "galaxies.txt"
         edgeGalFile = outputDir + "/galaxy_edge_flags.txt"
         contourFile = outputDir + "/contour_map.fits"
@@ -481,7 +482,7 @@ def launchZobov(sample, binPath, outputDir=None, logDir=None, continueRun=None,
       edgeFlags = np.loadtxt(edgeFile, dtype=np.int32)
 
       # set edge galaxy volumes to nearly 0 (implying very high density)
-      vols[ edgeFlags>0 ] = 1.e-4
+      vols[ edgeFlags>0 ] = 1.e-10
 
       volFile = outputDir+"/vol_weighted_"+sampleName+".dat"
       with open(volFile, mode='wb') as File:
@@ -493,7 +494,6 @@ def launchZobov(sample, binPath, outputDir=None, logDir=None, continueRun=None,
     else:
       volFileToUse = outputDir+"/vol_"+sampleName+".dat"
 
-
     cmd = [binPath+"/jozov2", \
            outputDir+"/adj_"+sampleName+".dat", \
            volFileToUse, \

python_source/backend/surveyTools.py

@@ -146,6 +146,7 @@ def findEdgeGalaxies(galFile, maskFile, edgeGalFile, contourFile,
 
   # load in galaxies
   #galPos = np.genfromtxt(galFile)
+  # TODO - WHY IS THIS FASTER THAN np.column_stack???
   galPos = np.genfromtxt(outputDir+"/galaxies.txt")
   with open(galFile, 'rb') as File:
    chk = np.fromfile(File, dtype=np.int32,count=1)

python_source/voidUtil/catalogUtil.py

@@ -484,6 +484,7 @@ def loadVoidCatalog(sampleDir, dataPortion="central", loadParticles=True,
             catalog.part[p].adjs.append(pAdj)
             catalog.part[pAdj].adjs.append(p)
 
+
     print(" Sanity checking adjacenies...")
     for p in range(numPart):
       catalog.part[p].nadjs = len(catalog.part[p].adjs)