Merge branch 'master' of bitbucket.org:cosmicvoids/void_identification

c_tools/analysis/voidOverlap.cpp

@@ -88,7 +88,7 @@ typedef struct catalog {
 
 void loadCatalog(const char *partFile, const char *volFile, 
                  const char *voidFile, const char *zoneFile,
-                 const char *infoFile, const char *barycenterFile,
+                 const char *infoFile, const char *centerFile,
                  const char *zonePartFile, CATALOG& catalog);
 
 float getDist(CATALOG& catalog1, CATALOG& catalog2, int& iVoid1, int& iVoid2,
@@ -110,7 +110,7 @@ int main(int argc, char **argv) {
   float closestMatchDist;
   float commonVolRatio;
   MATCHPROPS newMatch;
-  int MAX_MATCHES = 20;
+  int MAX_MATCHES = 10;
 
   CATALOG catalog1, catalog2;
 
@@ -136,11 +136,11 @@ int main(int argc, char **argv) {
   }
 
   loadCatalog(args.partFile1_arg, args.volFile1_arg, args.voidFile1_arg,
-              args.zoneFile1_arg, args.infoFile1_arg, args.barycenterFile1_arg,
+              args.zoneFile1_arg, args.infoFile1_arg, args.centerFile1_arg,
               args.zonePartFile1_arg, catalog1);
 
   loadCatalog(args.partFile2_arg, args.volFile2_arg, args.voidFile2_arg,
-              args.zoneFile2_arg, args.infoFile2_arg, args.barycenterFile2_arg,
+              args.zoneFile2_arg, args.infoFile2_arg, args.centerFile2_arg,
               args.zonePartFile2_arg, catalog2);
 
   // check for periodic box
@@ -164,7 +164,6 @@ int main(int argc, char **argv) {
       rdist = getDist(catalog1, catalog2, iVoid1, iVoid2, 
                       periodicX, periodicY, periodicZ);
 
-  
       newMatch.matchID = iVoid2;
       newMatch.commonVol = 0;
       newMatch.dist = rdist; 
@@ -319,7 +318,7 @@ int main(int argc, char **argv) {
                          //catalog1.voids[iVoid1].numPart;
                          catalog1.voids[iVoid1].vol;
 
-        fprintf(fp, "%.3f ", catalog1.voids[iVoid1].matches[iMatch].dist);
+        fprintf(fp, "%.3f %.2f ", catalog1.voids[iVoid1].matches[iMatch].dist, commonVolRatio);
         //fprintf(fp, "%.2f ", commonVolRatio);
       } else {
         fprintf(fp, "0.00 ");
@@ -339,7 +338,7 @@ int main(int argc, char **argv) {
 // ----------------------------------------------------------------------------
 void loadCatalog(const char *partFile, const char *volFile, 
                  const char *voidFile, const char *zoneFile,
-                 const char *infoFile, const char *barycenterFile,
+                 const char *infoFile, const char *centerFile,
                  const char *zonePartFile, CATALOG& catalog) {
 
   int i, p, numPartTot, numZonesTot, dummy, iVoid, iZ, numVolTot;
@@ -465,15 +464,22 @@ void loadCatalog(const char *partFile, const char *volFile,
   }
   fclose(fp);
 
+  catalog.numVoids = i - 1;
+  catalog.voids.resize(catalog.numVoids);
   printf("  Read %d voids.\n", catalog.numVoids);
 
   printf(" Loading barycenters\n");
-  fp = fopen(barycenterFile, "r");
+  fp = fopen(centerFile, "r");
   float tempBary[3];
+  float tempFloat;
+  int   tempInt;
   iVoid = 0;
   while (fgets(line, sizeof(line), fp) != NULL) {
-    sscanf(line, "%d %f %f %f\n", &voidID, &tempBary[0], &tempBary[1], 
+    sscanf(line, "%f %f %f %f %f %f %f %d %f %d %d %d\n", 
-                                  &tempBary[2]);
+           &tempBary[0], &tempBary[1], &tempBary[2],
+           &tempFloat, &tempFloat, &tempFloat, &tempFloat, &tempInt,
+           &tempFloat, &tempInt, &tempInt);
+
     tempBary[0] = (tempBary[0] - ranges[0][0])/catalog.boxLen[0];
     tempBary[1] = (tempBary[1] - ranges[1][0])/catalog.boxLen[1];
     tempBary[2] = (tempBary[2] - ranges[2][0])/catalog.boxLen[2];

c_tools/analysis/voidOverlap.ggo

@@ -10,7 +10,7 @@ option "voidFile1" -	"Void info file for catalog 1"	string yes
 option "infoFile1" -	"Extra info file for catalog 1"	string yes
 option "zoneFile1" - "Zone file for catalog 1"	string yes
 option "zonePartFile1" -	"Zone-particle file for catalog 1"	string yes
-option "barycenterFile1" - "Barycenter file for catalog 1" string yes
+option "centerFile1" - "Barycenter file for catalog 1" string yes
 
 # void data for file 2
 option "partFile2" - "Particle file for catalog 2"	string yes
@@ -19,7 +19,7 @@ option "voidFile2" - "Void info file for catalog 2"	string yes
 option "infoFile2" -	"Extra info file for catalog 2"	string yes
 option "zoneFile2" - "Zone file for catalog 2"	string yes
 option "zonePartFile2"	- "Zone-particle file for catalog 2"	string yes
-option "barycenterFile2" - "Barycenter file for catalog 2" string yes
+option "centerFile2" - "Barycenter file for catalog 2" string yes
 
 # options
 option "outfile" - "Output file" string yes

c_tools/stacking/pruneVoids.cpp

@@ -125,7 +125,7 @@ int main(int argc, char **argv) {
   }
 
   int i, p, p2, numPartTot, numZonesTot, dummy, iVoid, iZ;
-  int numVoids, mockIndex, numKept;
+  int numVoids, mockIndex;
   double tolerance;
   FILE *fp, *fpZobov, *fpCenters, *fpCentersNoCut, *fpBarycenter,
         *fpDistances, *fpShapes, *fpSkyPositions;
@@ -662,6 +662,21 @@ int main(int argc, char **argv) {
       voids[iVoid].isLeaf = true;
     }
   }
+
+// TEST - grabbing only top-level voids
+  numAreParents = 0;
+  iGood = 0;
+  for (iVoid = 0; iVoid < voids.size(); iVoid++) {
+    if (voids[iVoid].parentID != -1) {
+      numAreParents++;
+      voids[iVoid].isLeaf = false;
+     } else {
+      //voids[iGood++] = voids[iVoid];
+      voids[iVoid].isLeaf = true;
+    }
+  }
+// END TEST
+
   //voids.resize(iGood);
   //printf("  5th filter: rejected %d that are not leaf nodes\n", numAreParents); 
 
@@ -699,7 +714,7 @@ int main(int argc, char **argv) {
  
   name = "central"; 
   openFiles(outputDir, sampleName, name, 
-            mockIndex, numKept,
+            mockIndex, voids.size(),
             &fpZobov, &fpCenters, &fpCentersNoCut, &fpBarycenter, 
             &fpDistances, &fpShapes, &fpSkyPositions);
   
@@ -716,7 +731,7 @@ int main(int argc, char **argv) {
 
   name = "all";
   openFiles(outputDir, sampleName, name, 
-            mockIndex, numKept,
+            mockIndex, voids.size(),
             &fpZobov, &fpCenters, &fpCentersNoCut, &fpBarycenter, 
             &fpDistances, &fpShapes, &fpSkyPositions);
   for (iVoid = 0; iVoid < voids.size(); iVoid++) {
@@ -796,6 +811,35 @@ void outputVoid(int iVoid, VOID outVoid, FILE* fpZobov, FILE* fpCenters,
                 FILE* fpBarycenters, FILE* fpDistances, FILE* fpShapes,
                 bool isObservation, double *boxLen) {
 
+     double outCenter[3];
+     outCenter[0] = outVoid.barycenter[0];
+     outCenter[1] = outVoid.barycenter[1];
+     outCenter[2] = outVoid.barycenter[2];
+
+     if (isObservation) {
+       outCenter[0] = (outVoid.barycenter[0]-boxLen[0]/2.)*100.;
+       outCenter[1] = (outVoid.barycenter[1]-boxLen[1]/2.)*100.;
+       outCenter[2] = (outVoid.barycenter[2]-boxLen[2]/2.)*100.;
+     }
+
+  fprintf(fpCentersNoCut, "%.2f %.2f %.2f %.2f %.2f %.5f %.2f %d %f %d %d %d\n",
+             outCenter[0],
+             outCenter[1],
+             outCenter[2],
+             outVoid.vol,
+             outVoid.radius,
+             outVoid.redshift, 
+             4./3.*M_PI*pow(outVoid.radius, 3),
+             outVoid.voidID,
+             outVoid.densCon,
+             outVoid.numPart,
+             outVoid.parentID,
+             outVoid.numChildren);
+
+    if (outVoid.hasHighCentralDen || !outVoid.isLeaf) {
+       return;
+    } 
+
      fprintf(fpZobov, "%d %d %d %f %f %d %d %f %d %f %f\n", 
              iVoid, 
              outVoid.voidID, 
@@ -819,18 +863,6 @@ void outputVoid(int iVoid, VOID outVoid, FILE* fpZobov, FILE* fpCenters,
              outVoid.voidID, 
              outVoid.nearestMock);
 
-     double outCenter[3];
-     outCenter[0] = outVoid.barycenter[0];
-     outCenter[1] = outVoid.barycenter[1];
-     outCenter[2] = outVoid.barycenter[2];
-
-     if (isObservation) {
-       outCenter[0] = (outVoid.barycenter[0]-boxLen[0]/2.)*100.;
-       outCenter[1] = (outVoid.barycenter[1]-boxLen[1]/2.)*100.;
-       outCenter[2] = (outVoid.barycenter[2]-boxLen[2]/2.)*100.;
-     }
-
-     if (!outVoid.hasHighCentralDen && outVoid.isLeaf) {
        fprintf(fpCenters, "%.2f %.2f %.2f %.2f %.2f %.5f %.2f %d %f %d %d %d\n",
              outCenter[0],
              outCenter[1],
@@ -844,22 +876,7 @@ void outputVoid(int iVoid, VOID outVoid, FILE* fpZobov, FILE* fpCenters,
              outVoid.numPart,
              outVoid.parentID,
              outVoid.numChildren);
-     } 
+     
-
-       fprintf(fpCentersNoCut, "%.2f %.2f %.2f %.2f %.2f %.5f %.2f %d %f %d %d %d\n",
-             outCenter[0],
-             outCenter[1],
-             outCenter[2],
-             outVoid.vol,
-             outVoid.radius,
-             outVoid.redshift, 
-             4./3.*M_PI*pow(outVoid.radius, 3),
-             outVoid.voidID,
-             outVoid.densCon,
-             outVoid.numPart,
-             outVoid.parentID,
-             outVoid.numChildren);
-
      fprintf(fpSkyPositions, "%.2f %.2f %.5f %.2f %d\n",
              atan((outVoid.barycenter[1]-boxLen[1]/2.) / 
                   (outVoid.barycenter[0]-boxLen[0]/2.)) * 180/M_PI + 180,  

python_tools/void_python_tools/backend/launchers.py

@@ -394,8 +394,8 @@ def launchVoidOverlap(sample1, sample2, sample1Dir, sample2Dir,
            thisDataPortion+"_"+str(sampleName1)+".out"
     cmd += " --infoFile1=" + sample1Dir+"/zobov_slice_" + \
            str(sampleName1)+".par"
-    cmd += " --barycenterFile1=" + sample1Dir + \
+    cmd += " --centerFile1=" + sample1Dir + \
-           "/barycenters_"+thisDataPortion+"_"+str(sampleName1)+".out"
+           "/centers_"+thisDataPortion+"_"+str(sampleName1)+".out"
     cmd += " --zoneFile1=" + sample1Dir+"/voidZone_" + \
            str(sampleName1)+".dat"
     cmd += " --zonePartFile1=" + sample1Dir+"/voidPart_" + \
@@ -409,8 +409,8 @@ def launchVoidOverlap(sample1, sample2, sample1Dir, sample2Dir,
            thisDataPortion+"_"+str(sampleName2)+".out"
     cmd += " --infoFile2=" + sample2Dir+"/zobov_slice_" + \
            str(sampleName2)+".par"
-    cmd += " --barycenterFile2=" + sample2Dir + \
+    cmd += " --centerFile2=" + sample2Dir + \
-           "/barycenters_"+thisDataPortion+"_"+str(sampleName2)+".out"
+           "/centers_"+thisDataPortion+"_"+str(sampleName2)+".out"
     cmd += " --zoneFile2=" + sample2Dir+"/voidZone_" + \
            str(sampleName2)+".dat"
     cmd += " --zonePartFile2=" + sample2Dir+"/voidPart_" + \