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

analysis/datasetsToAnalyze.py

@@ -1,5 +1,5 @@
 #+
-#   VIDE -- Void IDEntification pipeline -- ./crossCompare/analysis/datasetsToAnalyze.py
+#   VIDE -- Void IDentification and Examination -- ./crossCompare/analysis/datasetsToAnalyze.py
 #   Copyright (C) 2010-2013 Guilhem Lavaux
 #   Copyright (C) 2011-2013 P. M. Sutter
 #

analysis/xcor.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 #+
-#   VIDE -- Void IDEntification pipeline -- ./crossCompare/analysis/mergerTree.py
+#   VIDE -- Void IDentification and Examination -- ./crossCompare/analysis/mergerTree.py
 #   Copyright (C) 2010-2013 Guilhem Lavaux
 #   Copyright (C) 2011-2013 P. M. Sutter
 #

build_tools/gather_sources.py

@@ -1,5 +1,5 @@
 #+
-#   VIDE -- Void IDEntification pipeline -- ./build_tools/gather_sources.py
+#   VIDE -- Void IDentification and Examination -- ./build_tools/gather_sources.py
 #   Copyright (C) 2010-2013 Guilhem Lavaux
 #   Copyright (C) 2011-2013 P. M. Sutter
 #
@@ -40,7 +40,7 @@ def apply_license(license, relimit, filename):
 
 def apply_python_license(filename):
   license="""#+
-#   VIDE -- Void IDEntification pipeline -- @FILENAME@
+#   VIDE -- Void IDentification and Examination -- @FILENAME@
 #   Copyright (C) 2010-2013 Guilhem Lavaux
 #   Copyright (C) 2011-2013 P. M. Sutter
 #
@@ -67,7 +67,7 @@ def apply_python_license(filename):
 
 def apply_cpp_license(filename):
   license="""/*+
-    VIDE -- Void IDEntification pipeline -- @FILENAME@
+    VIDE -- Void IDentification and Examination -- @FILENAME@
     Copyright (C) 2010-2013 Guilhem Lavaux
     Copyright (C) 2011-2013 P. M. Sutter
 

c_tools/analysis/voidOverlap.cpp

@@ -1,5 +1,5 @@
 /*+
-    VIDE -- Void IDEntification pipeline -- ./c_tools/analysis/voidOverlap.cpp
+    VIDE -- Void IDentification and Examination -- ./c_tools/analysis/voidOverlap.cpp
     Copyright (C) 2010-2013 Guilhem Lavaux
     Copyright (C) 2011-2013 P. M. Sutter
 
@@ -73,6 +73,7 @@ typedef struct voidStruct {
   float nearestEdge;
   float barycenter[3];
   float ellipticity;
+  float eigv1[3], eigv2[3], eigv3[3], eig[3];
   std::vector<MATCHPROPS> matches;
   int numMatches;
   int numBigMatches;
@@ -375,6 +376,87 @@ int main(int argc, char **argv) {
                      catalog1.voids[iVoid1].radius;
       float ellipRatio = catalog2.voids[iVoid2].ellipticity / 
                          catalog1.voids[iVoid1].ellipticity;
+
+      // find angles between major axes, etc.
+     int iMaj1, iMed1, iMin1;
+     int iMaj2, iMed2, iMin2;
+     float eig1[3], eig2[3];
+     float eigv1[6], eigv2[6];
+     float cosThetaMaj, cosThetaMed, cosThetaMin;
+ 
+     for (int i = 0; i < 3; i++) {
+       eig1[i] = catalog1.voids[iVoid1].eig[i];
+       eigv1[0,i] = catalog1.voids[iVoid1].eigv1[i];
+       eigv1[1,i] = catalog1.voids[iVoid1].eigv2[i];
+       eigv1[2,i] = catalog1.voids[iVoid1].eigv3[i];
+       eig2[i] = catalog2.voids[iVoid2].eig[i];
+       eigv2[0,i] = catalog2.voids[iVoid2].eigv1[i];
+       eigv2[1,i] = catalog2.voids[iVoid2].eigv2[i];
+       eigv2[2,i] = catalog2.voids[iVoid2].eigv3[i];
+     }
+  
+     if (eig1[0] > eig1[1] && eig1[0] > eig1[2]) iMaj1 = 0;
+     if (eig1[1] > eig1[2] && eig1[1] > eig1[0]) iMaj1 = 1;
+     if (eig1[2] > eig1[1] && eig1[2] > eig1[0]) iMaj1 = 2;
+     if (eig1[0] > eig1[1] && eig1[0] < eig1[2]) iMed1 = 0;
+     if (eig1[1] > eig1[2] && eig1[1] < eig1[0]) iMed1 = 1;
+     if (eig1[2] > eig1[1] && eig1[2] < eig1[0]) iMed1 = 2;
+     if (eig1[0] < eig1[1] && eig1[0] < eig1[2]) iMin1 = 0;
+     if (eig1[1] < eig1[2] && eig1[1] < eig1[0]) iMin1 = 1;
+     if (eig1[2] < eig1[1] && eig1[2] < eig1[0]) iMin1 = 2;
+
+     if (eig2[0] > eig2[1] && eig2[0] > eig2[2]) iMaj2 = 0;
+     if (eig2[1] > eig2[2] && eig2[1] > eig2[0]) iMaj2 = 1;
+     if (eig2[2] > eig2[1] && eig2[2] > eig2[0]) iMaj2 = 2;
+     if (eig2[0] > eig2[1] && eig2[0] < eig2[2]) iMed2 = 0;
+     if (eig2[1] > eig2[2] && eig2[1] < eig2[0]) iMed2 = 1;
+     if (eig2[2] > eig2[1] && eig2[2] < eig2[0]) iMed2 = 2;
+     if (eig2[0] < eig2[1] && eig2[0] < eig2[2]) iMin2 = 0;
+     if (eig2[1] < eig2[2] && eig2[1] < eig2[0]) iMin2 = 1;
+     if (eig2[2] < eig2[1] && eig2[2] < eig2[0]) iMin2 = 2;
+
+//printf("EIG CHECK %d %d %e %e %e %d %e %e %e %d\n", iVoid1, iVoid2, eig1[0], eig1[1], eig1[2], iMin1, eig2[0], eig2[1], eig2[2], iMin2);
+     cosThetaMaj = (eigv1[iMaj1,0]*eigv2[iMaj2,0] + 
+                          eigv1[iMaj1,1]*eigv2[iMaj2,1] +    
+                          eigv1[iMaj1,2]*eigv2[iMaj2,2]);
+//printf("EIG CHECK %d %d %e %e %e %e %e %e %e\n", iVoid1, iVoid2, eigv1[iMaj1,0], eigv1[iMaj1,1], eigv1[iMaj1,2], eigv2[iMaj2,0], eigv2[iMaj2,1], eigv2[iMaj2,2], cosThetaMaj);
+
+  
+     if (fabs(cosThetaMaj) > 0.) cosThetaMaj = acos(fabs(cosThetaMaj));
+
+     float majAxisRatio = eig2[iMaj2]/eig1[iMaj1];
+     float minAxisRatio = eig2[iMin2]/eig1[iMin1];
+
+// TEST 
+/*
+  if (catalog1.voids[iVoid1].voidID == 267 &&
+      catalog2.voids[iVoid2].voidID == 346) {
+
+    int voidID1 = catalog1.voids[iVoid1].voidID;
+    for (iZ1 = 0; iZ1 < catalog1.void2Zones[voidID1].numZones; iZ1++) {
+      zoneID1 = catalog1.void2Zones[voidID1].zoneIDs[iZ1];
+      for (p1 = 0; p1 < catalog1.zones2Parts[zoneID1].numPart; p1++) {
+        partID1 = catalog1.zones2Parts[zoneID1].partIDs[p1];     
+        printf("VOID1 %e %e %e\n", catalog1.part[partID1].x,
+                                       catalog1.part[partID1].y,
+                                       catalog1.part[partID1].z);
+      }
+    }
+
+    int voidID2 = catalog2.voids[iVoid2].voidID;
+    for (iZ2 = 0; iZ2 < catalog2.void2Zones[voidID2].numZones; iZ2++) {
+      zoneID2 = catalog2.void2Zones[voidID2].zoneIDs[iZ2];
+      for (p2 = 0; p2 < catalog2.zones2Parts[zoneID2].numPart; p2++) {
+        partID2 = catalog2.zones2Parts[zoneID2].partIDs[p2];     
+        printf("VOID1 %e %e %e\n", catalog2.part[partID2].x,
+                                       catalog2.part[partID2].y,
+                                       catalog2.part[partID2].z);
+      }
+    }
+  
+  }
+*/
+// END TEST
       commonVolRatio = catalog1.voids[iVoid1].matches[0].commonVolOrig / 
                        //catalog1.voids[iVoid1].numPart;
                        catalog1.voids[iVoid1].vol;
@@ -383,7 +465,7 @@ int main(int argc, char **argv) {
       rdist = catalog1.voids[iVoid1].matches[0].dist;
       rdist /= catalog1.voids[iVoid1].radius;
 
-      fprintf(fp, "%d %.4f %.4f %e %e %.4f %d %d %d %e %e %e\n", voidID, 
+      fprintf(fp, "%d %.4f %.4f %e %e %.4f %d %d %d %e %e %e %e %e %e\n", voidID, 
       //fprintf(fp, "%d %.4f %.4f %.4f %.4f %.4f %d %d %d\n", voidID, 
                                    catalog1.voids[iVoid1].radiusMpc,
                                    rRatio, 
@@ -395,10 +477,14 @@ int main(int argc, char **argv) {
                                    catalog2.voids[iVoid2].voidID,
                                    catalog1.voids[iVoid1].matches[0].merit,
                                    ellipRatio,
-                                   catalog1.voids[iVoid1].densCon);
+                                   catalog1.voids[iVoid1].densCon,
+                                   cosThetaMaj,
+                                   majAxisRatio,
+                                   minAxisRatio
+                                   );
 
     } else {
-      fprintf(fp, "%d %.4f 0.0 0.0 0.0 0.0 0.0 0 0 0 0.0 0.0\n", voidID, 
+      fprintf(fp, "%d %.4f 0.0 0.0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0.0 0.0\n", voidID, 
                                            catalog1.voids[iVoid1].radiusMpc);
     }
   } // end printing
@@ -601,17 +687,29 @@ void loadCatalog(const char *partFile, const char *volFile,
   printf(" Loading shapes\n");
   fp = fopen(shapeFile, "r");
   iVoid = 0;
-  float tempEllip;
+  float tempEllip, eig[3], eigv1[3], eigv2[3], eigv3[3];
   fgets(line, sizeof(line), fp);
   while (fgets(line, sizeof(line), fp) != NULL) {
     sscanf(line, "%d %f %f %f %f %f %f %f %f %f %f %f %f %f\n", 
-           &tempInt, &tempEllip, &tempFloat, &tempFloat, &tempFloat,
+           &tempInt, &tempEllip, &eig[0], &eig[1], &eig[2],
-           &tempFloat, &tempFloat, &tempFloat,
+           &eigv1[0], &eigv1[1], &eigv1[2],
-           &tempFloat, &tempFloat, &tempFloat,
+           &eigv2[0], &eigv2[1], &eigv2[2],
-           &tempFloat, &tempFloat, &tempFloat);
+           &eigv3[0], &eigv3[1], &eigv3[2]);
 
 //if (iVoid < 10) printf("SHAPE %d %d %e\n", iVoid, catalog.voids[iVoid].voidID, tempEllip);
     catalog.voids[iVoid].ellipticity = tempEllip;
+    catalog.voids[iVoid].eig[0] = eig[0];
+    catalog.voids[iVoid].eig[1] = eig[1];
+    catalog.voids[iVoid].eig[2] = eig[2];
+    catalog.voids[iVoid].eigv1[0] = eigv1[0];
+    catalog.voids[iVoid].eigv1[1] = eigv1[1];
+    catalog.voids[iVoid].eigv1[2] = eigv1[2];
+    catalog.voids[iVoid].eigv2[0] = eigv2[0];
+    catalog.voids[iVoid].eigv2[1] = eigv2[1];
+    catalog.voids[iVoid].eigv2[2] = eigv2[2];
+    catalog.voids[iVoid].eigv3[0] = eigv3[0];
+    catalog.voids[iVoid].eigv3[1] = eigv3[1];
+    catalog.voids[iVoid].eigv3[2] = eigv3[2];
     iVoid++;
   }
   fclose(fp);

c_tools/libzobov/contour_pixels.cpp

@@ -1,5 +1,5 @@
 /*+
-    VIDE -- Void IDEntification pipeline -- ./c_tools/libzobov/contour_pixels.cpp
+    VIDE -- Void IDentification and Examination -- ./c_tools/libzobov/contour_pixels.cpp
     Copyright (C) 2010-2013 Guilhem Lavaux
     Copyright (C) 2011-2013 P. M. Sutter
 

c_tools/libzobov/loadZobov.cpp

@@ -1,5 +1,5 @@
 /*+
-    VIDE -- Void IDEntification pipeline -- ./c_tools/libzobov/loadZobov.cpp
+    VIDE -- Void IDentification and Examination -- ./c_tools/libzobov/loadZobov.cpp
     Copyright (C) 2010-2013 Guilhem Lavaux
     Copyright (C) 2011-2013 P. M. Sutter
 
@@ -168,6 +168,13 @@ bool loadZobov(const char *descName, const char *adjName, const char *voidsName,
 	  abort();
 	}
     
+/*  
+    sscanf(line.c_str(), "%d %d %d %f %f %d %d %f %d %f %f\n", &orderId, &volId,
+           &coreParticle, &coreDensity, &volumeZone, &numParticlesInZone, 
+           &numZonesInVoid,
+           &volumeVoid, &numInVoid, &densityContrast, &probability);
+*/
+
       z.allVoids[volId].proba = probability;
       z.allVoids[volId].volume = volumeVoid;
       z.allVoids[volId].numParticles = numInVoid;

c_tools/libzobov/particleInfo.cpp

@@ -1,5 +1,5 @@
 /*+
-    VIDE -- Void IDEntification pipeline -- ./c_tools/libzobov/particleInfo.cpp
+    VIDE -- Void IDentification and Examination -- ./c_tools/libzobov/particleInfo.cpp
     Copyright (C) 2010-2013 Guilhem Lavaux
     Copyright (C) 2011-2013 P. M. Sutter
 
@@ -93,21 +93,25 @@ bool loadParticleInfo(ParticleInfo& info,
       info.particles.resize(numpart);
       
       offset = info.ranges[0][0];
-      mul = info.ranges[0][1] - info.ranges[0][0];
+      // TEST PMS NON-COBIC BOXES
+      mul = 1.0;
+      //mul = info.ranges[0][1] - info.ranges[0][0];
       f.beginCheckpoint();
       for (int i = 0; i < numpart; i++)
 	info.particles[i].x = mul*f.readReal32();
       f.endCheckpoint();
       
       offset = info.ranges[1][0];
-      mul = info.ranges[1][1] - info.ranges[1][0];
+      mul = 1.0;
+      //mul = info.ranges[1][1] - info.ranges[1][0];
       f.beginCheckpoint();
       for (int i = 0; i < numpart; i++)
 	info.particles[i].y = mul*f.readReal32();
       f.endCheckpoint();
       
       offset = info.ranges[2][0];
-      mul = info.ranges[2][1] - info.ranges[2][0];
+      mul = 1.0;
+      //mul = info.ranges[2][1] - info.ranges[2][0];
       f.beginCheckpoint();
       for (int i = 0; i < numpart; i++)
 	info.particles[i].z = mul*f.readReal32();

c_tools/mock/generateFromCatalog.cpp

@@ -1,5 +1,5 @@
 /*+
-    VIDE -- Void IDEntification pipeline -- ./c_tools/mock/generateFromCatalog.cpp
+    VIDE -- Void IDentification and Examination -- ./c_tools/mock/generateFromCatalog.cpp
     Copyright (C) 2010-2013 Guilhem Lavaux
     Copyright (C) 2011-2013 P. M. Sutter
 
@@ -369,7 +369,7 @@ void generateSurfaceMask(generateFromCatalog_info& args ,
   fp = fopen("mock_sphere.txt", "w");
 
   for (int q = 0; q < 0; q++) {
-    //for (int p = 0; p < full_mask_list.size(); p++) {
+  //for (int q = 0; q < full_mask_list.size(); q++) {
     vec3 v = mask.pix2vec(full_mask_list[q]);
 	  
     Position p;

c_tools/mock/generateMock.cpp

@@ -1,5 +1,5 @@
 /*+
-    VIDE -- Void IDEntification pipeline -- ./c_tools/mock/generateMock.cpp
+    VIDE -- Void IDentification and Examination -- ./c_tools/mock/generateMock.cpp
     Copyright (C) 2010-2013 Guilhem Lavaux
     Copyright (C) 2011-2013 P. M. Sutter
 

c_tools/mock/generateTestMock.cpp

@@ -1,5 +1,5 @@
 /*+
-    VIDE -- Void IDEntification pipeline -- ./c_tools/mock/generateTestMock.cpp
+    VIDE -- Void IDentification and Examination -- ./c_tools/mock/generateTestMock.cpp
     Copyright (C) 2010-2013 Guilhem Lavaux
     Copyright (C) 2011-2013 P. M. Sutter
 

c_tools/mock/loaders/basic_loader.cpp

@@ -1,5 +1,5 @@
 /*+
-    VIDE -- Void IDEntification pipeline -- ./c_tools/mock/loaders/basic_loader.cpp
+    VIDE -- Void IDentification and Examination -- ./c_tools/mock/loaders/basic_loader.cpp
     Copyright (C) 2010-2013 Guilhem Lavaux
     Copyright (C) 2011-2013 P. M. Sutter
 

c_tools/mock/loaders/flash_loader.cpp

@@ -1,5 +1,5 @@
 /*+
-    VIDE -- Void IDEntification pipeline -- ./c_tools/mock/loaders/flash_loader.cpp
+    VIDE -- Void IDentification and Examination -- ./c_tools/mock/loaders/flash_loader.cpp
     Copyright (C) 2010-2013 Guilhem Lavaux
     Copyright (C) 2011-2013 P. M. Sutter
 

c_tools/mock/loaders/gadget_loader.cpp

@@ -1,5 +1,5 @@
 /*+
-    VIDE -- Void IDEntification pipeline -- ./c_tools/mock/loaders/gadget_loader.cpp
+    VIDE -- Void IDentification and Examination -- ./c_tools/mock/loaders/gadget_loader.cpp
     Copyright (C) 2010-2013 Guilhem Lavaux
     Copyright (C) 2011-2013 P. M. Sutter
 

c_tools/mock/loaders/multidark_loader.cpp

@@ -1,5 +1,5 @@
 /*+
-    VIDE -- Void IDEntification pipeline -- ./c_tools/mock/loaders/multidark_loader.cpp
+    VIDE -- Void IDentification and Examination -- ./c_tools/mock/loaders/multidark_loader.cpp
     Copyright (C) 2010-2013 Guilhem Lavaux
     Copyright (C) 2011-2013 P. M. Sutter
 

c_tools/mock/loaders/ramses_loader.cpp

@@ -1,5 +1,5 @@
 /*+
-    VIDE -- Void IDEntification pipeline -- ./c_tools/mock/loaders/ramses_loader.cpp
+    VIDE -- Void IDentification and Examination -- ./c_tools/mock/loaders/ramses_loader.cpp
     Copyright (C) 2010-2013 Guilhem Lavaux
     Copyright (C) 2011-2013 P. M. Sutter
 

c_tools/mock/loaders/sdf_loader.cpp

@@ -1,5 +1,5 @@
 /*+
-    VIDE -- Void IDEntification pipeline -- ./c_tools/mock/loaders/sdf_loader.cpp
+    VIDE -- Void IDentification and Examination -- ./c_tools/mock/loaders/sdf_loader.cpp
     Copyright (C) 2010-2013 Guilhem Lavaux
     Copyright (C) 2011-2013 P. M. Sutter
 

c_tools/mock/loaders/simulation_loader.cpp

@@ -1,5 +1,5 @@
 /*+
-    VIDE -- Void IDEntification pipeline -- ./c_tools/mock/loaders/simulation_loader.cpp
+    VIDE -- Void IDentification and Examination -- ./c_tools/mock/loaders/simulation_loader.cpp
     Copyright (C) 2010-2013 Guilhem Lavaux
     Copyright (C) 2011-2013 P. M. Sutter
 

c_tools/stacking/pruneVoids.cpp

@@ -1,5 +1,5 @@
 /*+
-    VIDE -- Void IDEntification pipeline -- ./c_tools/stacking/pruneVoids.cpp
+    VIDE -- Void IDentification and Examination -- ./c_tools/stacking/pruneVoids.cpp
     Copyright (C) 2010-2013 Guilhem Lavaux
     Copyright (C) 2011-2013 P. M. Sutter
 

crossCompare/analysis/makeCocenterProfiles.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 #+
-#   VIDE -- Void IDEntification pipeline -- ./pipeline/apAnalysis.py
+#   VIDE -- Void IDentification and Examination -- ./pipeline/apAnalysis.py
 #   Copyright (C) 2010-2013 Guilhem Lavaux
 #   Copyright (C) 2011-2013 P. M. Sutter
 #

crossCompare/analysis/overlapVoids.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 #+
-#   VIDE -- Void IDEntification pipeline -- ./crossCompare/analysis/mergerTree.py
+#   VIDE -- Void IDentification and Examination -- ./crossCompare/analysis/mergerTree.py
 #   Copyright (C) 2010-2013 Guilhem Lavaux
 #   Copyright (C) 2011-2013 P. M. Sutter
 #

crossCompare/plotting/plotCocenterProfiles.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 #+
-#   VIDE -- Void IDEntification pipeline -- ./pipeline/apAnalysis.py
+#   VIDE -- Void IDentification and Examination -- ./pipeline/apAnalysis.py
 #   Copyright (C) 2010-2013 Guilhem Lavaux
 #   Copyright (C) 2011-2013 P. M. Sutter
 #

crossCompare/plotting/plotDenMaps.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 #+
-#   VIDE -- Void IDEntification pipeline -- ./pipeline/apAnalysis.py
+#   VIDE -- Void IDentification and Examination -- ./pipeline/apAnalysis.py
 #   Copyright (C) 2010-2013 Guilhem Lavaux
 #   Copyright (C) 2011-2013 P. M. Sutter
 #

pipeline/generateCatalog.py

@@ -77,31 +77,6 @@ for sample in dataSampleList:
   if not os.access(zobovDir, os.F_OK):
     os.makedirs(zobovDir)
 
-  # save this sample's information
-  with open(zobovDir+"/sample_info.dat", 'w') as output:
-    pickle.dump(sample, output, pickle.HIGHEST_PROTOCOL)
-
-  fp = open(zobovDir+"/sample_info.txt", 'w')
-  fp.write("Sample name: %s\n" % sample.fullName)
-  fp.write("Sample nickname: %s\n" % sample.nickName)
-  fp.write("Data type: %s\n" % sample.dataType)
-  fp.write("Redshift range: %f - %f\n" %(sample.zBoundary[0],sample.zBoundary[1]))
-
-  #fp.write("Estimated mean particle separation: %g\n" % sample.minVoidRadius)
-
-  if (sample.dataType == "simulation"):
-    fp.write("Particles placed on lightcone: %g\n" % sample.useLightCone)
-    fp.write("Peculiar velocities included: %g\n" % sample.usePecVel)
-    if (len(sample.subsample) == 1):
-      fp.write("Additional subsampling fraction: %s\n" % sample.subsample)
-    else:
-      fp.write("Additional subsampling fraction: %s\n" % sample.subsample[-1])
-    fp.write("Simulation box length (Mpc/h): %g\n" % sample.boxLen)
-    fp.write("Simulation Omega_M: %g\n" % sample.omegaM)
-    fp.write("Number of simulation subvolumes: %s\n" % sample.numSubvolumes)
-    fp.write("My subvolume index: %s\n" % sample.mySubvolume)
-  fp.close()
-
 # ---------------------------------------------------------------------------
   if (startCatalogStage <= 1) and (endCatalogStage >= 1) and not sample.isCombo:
     print "  Extracting tracers from catalog...",

python_tools/pipeline_source/defaults.py

@@ -1,5 +1,5 @@
 #+
-#   VIDE -- Void IDEntification pipeline -- ./pipeline/datasets/mergertree.py
+#   VIDE -- Void IDentification and Examination -- ./pipeline/datasets/mergertree.py
 #   Copyright (C) 2010-2013 Guilhem Lavaux
 #   Copyright (C) 2011-2013 P. M. Sutter
 #
@@ -121,6 +121,7 @@ haloFileVYCol = 4
 haloFileVZCol = 5
 haloFileColSep = ','
 haloFileNumComLines = 0
+haloFilePosRescale = 1.0 # rescaling necessary to get Mpc/h
 
 # adjust these two parameters given the memory contraints on your system:
 #   numZobovDivisions: how many sub-volumes per dimension will zobov process

python_tools/pipeline_source/prepareCatalogs.in.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 #+
-#   VIDE -- Void IDEntification pipeline -- ./python_tools/pipeline_source/prepareCatalogs.in.py
+#   VIDE -- Void IDentification and Examination -- ./python_tools/pipeline_source/prepareCatalogs.in.py
 #   Copyright (C) 2010-2013 Guilhem Lavaux
 #   Copyright (C) 2011-2013 P. M. Sutter
 #
@@ -143,6 +143,7 @@ startAPStage = {startAPStage}
 endAPStage = {endAPStage}
 
 regenerateFlag = False
+#ZOBOV_PATH = "@CMAKE_BINARY_DIR@/c_tools/zobov2/"
 ZOBOV_PATH = "@CMAKE_BINARY_DIR@/zobov/"
 CTOOLS_PATH = "@CMAKE_BINARY_DIR@/c_tools/"
 freshStack = True
@@ -180,6 +181,7 @@ numZobovThreads = {numZobovThreads}
                                    numZobovDivisions=numZobovDivisions,
                                    numZobovThreads=numZobovThreads))
 
+
   sampleInfo = """
 newSample = Sample(dataFile = "{dataFile}",
                    dataFormat = "{dataFormat}",
@@ -195,6 +197,7 @@ newSample = Sample(dataFile = "{dataFile}",
                    profileBinSize = "auto",
                    includeInHubble = True,
                    partOfCombo = False,
+                   {autoStack}
                    isCombo = False,
                    boxLen = {boxLen},
                    usePecVel = {usePecVel},
@@ -212,24 +215,46 @@ newSample.addStack(0.0, 5.0, 5 , 10, False, False, rescaleMode="rv")
 newSample.addStack(0.0, 5.0, 10, 15, False, False, rescaleMode="rv")
 newSample.addStack(0.0, 5.0, 15, 20, False, False, rescaleMode="rv")
 newSample.addStack(0.0, 5.0, 20, 25, False, False, rescaleMode="rv")
+newSample.addStack(0.0, 5.0, 25, 30, False, False, rescaleMode="rv")
 newSample.addStack(0.0, 5.0, 30, 35, False, False, rescaleMode="rv")
+newSample.addStack(0.0, 5.0, 35, 40, False, False, rescaleMode="rv")
 newSample.addStack(0.0, 5.0, 40, 45, False, False, rescaleMode="rv")
+newSample.addStack(0.0, 5.0, 45, 50, False, False, rescaleMode="rv")
 newSample.addStack(0.0, 5.0, 50, 55, False, False, rescaleMode="rv")
+newSample.addStack(0.0, 5.0, 55, 60, False, False, rescaleMode="rv")
 newSample.addStack(0.0, 5.0, 60, 65, False, False, rescaleMode="rv")
+newSample.addStack(0.0, 5.0, 65, 70, False, False, rescaleMode="rv")
 newSample.addStack(0.0, 5.0, 70, 75, False, False, rescaleMode="rv")
+newSample.addStack(0.0, 5.0, 75, 80, False, False, rescaleMode="rv")
 newSample.addStack(0.0, 5.0, 80, 85, False, False, rescaleMode="rv")
+newSample.addStack(0.0, 5.0, 85, 90, False, False, rescaleMode="rv")
 newSample.addStack(0.0, 5.0, 90, 95, False, False, rescaleMode="rv")
+newSample.addStack(0.0, 5.0, 95, 100, False, False, rescaleMode="rv")
   """
 
-  elif stackMode == "auto":
+  elif stackMode == "log":
-    stackInfo = """
+    stackInfo = ""
-newSample.addStack({zMin}, {zMax}, 2*{minRadius}  , 2*{minRadius}+2, True, False, rescaleMode="rv")
+    rMin = 10
-newSample.addStack({zMin}, {zMax}, 2*{minRadius}  , 2*{minRadius}+4, True, False, rescaleMode="rv")
+    rMax = 100
-newSample.addStack({zMin}, {zMax}, 2*{minRadius}+2, 2*{minRadius}+6, True, False, rescaleMode="rv")
+    rStart = rMin
-newSample.addStack({zMin}, {zMax}, 2*{minRadius}+6, 2*{minRadius}+10, True, False, rescaleMode="rv")
+    rEnd = rMin
-newSample.addStack({zMin}, {zMax}, 2*{minRadius}+10, 2*{minRadius}+18, True, False, rescaleMode="rv")
+    dlogR = 0.25
-newSample.addStack({zMin}, {zMax}, 2*{minRadius}+18, 2*{minRadius}+24, True, False, rescaleMode="rv")
+    while rEnd < rMax:
-               """
+      rEnd = (1+0.5*dlogR)*rStart/(1-0.5*dlogR)
+    
+      stackInfo += """newSample.addStack({zMin}, {zMax}"""+ ", %g, %g, True, False, rescaleMode='rv')" % (rStart, rEnd)
+      
+      rStart = rEnd
+
+#  elif stackMode == "auto":
+#    stackInfo = """
+#newSample.addStack({zMin}, {zMax}, 2*{minRadius}  , 2*{minRadius}+2, True, False, rescaleMode="rv")
+#newSample.addStack({zMin}, {zMax}, 2*{minRadius}  , 2*{minRadius}+4, True, False, rescaleMode="rv")
+#newSample.addStack({zMin}, {zMax}, 2*{minRadius}+2, 2*{minRadius}+6, True, False, rescaleMode="rv")
+#newSample.addStack({zMin}, {zMax}, 2*{minRadius}+6, 2*{minRadius}+10, True, False, rescaleMode="rv")
+#newSample.addStack({zMin}, {zMax}, 2*{minRadius}+10, 2*{minRadius}+18, True, False, rescaleMode="rv")
+#newSample.addStack({zMin}, {zMax}, 2*{minRadius}+18, 2*{minRadius}+24, True, False, rescaleMode="rv")
+#               """
   else:
     stackInfo = """
 # {zMin}, {zMax}, {minRadius}
@@ -286,6 +311,8 @@ newSample.addStack({zMin}, {zMax}, 2*{minRadius}+18, 2*{minRadius}+24, True, Fal
           nickName = getNickName(setName, sampleName)
 
 
+          autoStack = ""
+          if stackMode == "auto": autoStack = "autoNumInStack = 400,"
           scriptFile.write(sampleInfo.format(dataFile=dataFileName,
                                          dataFormat=dataFormat,
                                          dataUnit=dataUnit,
@@ -297,6 +324,7 @@ newSample.addStack({zMin}, {zMax}, 2*{minRadius}+18, 2*{minRadius}+24, True, Fal
                                          zMaxMpc=sliceMaxMpc,
                                          omegaM=Om,
                                          boxLen=lbox,
+                                         autoStack=autoStack,
                                          usePecVel=useVel,
                                          minRadius=minRadius,
                                          numSubvolumes=numSubvolumes,
@@ -653,9 +681,9 @@ if (args.halos or args.all) and haloFileBase != "":
           if iHalo < haloFileNumComLines: continue
           line = line.split(haloFileColSep)
           if minHaloMass == "none" or float(line[haloFileMCol]) > minHaloMass:
-            x  = float(line[haloFileXCol])
+            x  = float(line[haloFileXCol]) * haloFilePosRescale
-            y  = float(line[haloFileYCol])
+            y  = float(line[haloFileYCol]) * haloFilePosRescale
-            z  = float(line[haloFileZCol])
+            z  = float(line[haloFileZCol]) * haloFilePosRescale
             vz = float(line[haloFileVZCol])
             vy = float(line[haloFileVYCol])
             vx = float(line[haloFileVXCol])

python_tools/setup.py

@@ -1,5 +1,5 @@
 #+
-#   VIDE -- Void IDEntification pipeline -- ./python_tools/setup.py
+#   VIDE -- Void IDentification and Examination -- ./python_tools/setup.py
 #   Copyright (C) 2010-2013 Guilhem Lavaux
 #   Copyright (C) 2011-2013 P. M. Sutter
 #

python_tools/void_python_tools/__init__.py

@@ -1,5 +1,5 @@
 #+
-#   VIDE -- Void IDEntification pipeline -- ./python_tools/void_python_tools/__init__.py
+#   VIDE -- Void IDentification and Examination -- ./python_tools/void_python_tools/__init__.py
 #   Copyright (C) 2010-2013 Guilhem Lavaux
 #   Copyright (C) 2011-2013 P. M. Sutter
 #

python_tools/void_python_tools/apTools/__init__.py

@@ -1,5 +1,5 @@
 #+
-#   VIDE -- Void IDEntification pipeline -- ./python_tools/void_python_tools/apTools/__init__.py
+#   VIDE -- Void IDentification and Examination -- ./python_tools/void_python_tools/apTools/__init__.py
 #   Copyright (C) 2010-2013 Guilhem Lavaux
 #   Copyright (C) 2011-2013 P. M. Sutter
 #

python_tools/void_python_tools/apTools/chi2/__init__.py

@@ -1,5 +1,5 @@
 #+
-#   VIDE -- Void IDEntification pipeline -- ./python_tools/void_python_tools/apTools/chi2/__init__.py
+#   VIDE -- Void IDentification and Examination -- ./python_tools/void_python_tools/apTools/chi2/__init__.py
 #   Copyright (C) 2010-2013 Guilhem Lavaux
 #   Copyright (C) 2011-2013 P. M. Sutter
 #

python_tools/void_python_tools/apTools/chi2/cosmologyTools.py

@@ -1,5 +1,5 @@
 #+
-#   VIDE -- Void IDEntification pipeline -- ./python_tools/void_python_tools/apTools/chi2/cosmologyTools.py
+#   VIDE -- Void IDentification and Examination -- ./python_tools/void_python_tools/apTools/chi2/cosmologyTools.py
 #   Copyright (C) 2010-2013 Guilhem Lavaux
 #   Copyright (C) 2011-2013 P. M. Sutter
 #

python_tools/void_python_tools/apTools/profiles/__init__.py

@@ -1,5 +1,5 @@
 #+
-#   VIDE -- Void IDEntification pipeline -- ./python_tools/void_python_tools/apTools/profiles/__init__.py
+#   VIDE -- Void IDentification and Examination -- ./python_tools/void_python_tools/apTools/profiles/__init__.py
 #   Copyright (C) 2010-2013 Guilhem Lavaux
 #   Copyright (C) 2011-2013 P. M. Sutter
 #

python_tools/void_python_tools/apTools/profiles/getSurveyProps.py

@@ -1,5 +1,5 @@
 #+
-#   VIDE -- Void IDEntification pipeline -- ./python_tools/void_python_tools/apTools/profiles/getSurveyProps.py
+#   VIDE -- Void IDentification and Examination -- ./python_tools/void_python_tools/apTools/profiles/getSurveyProps.py
 #   Copyright (C) 2010-2013 Guilhem Lavaux
 #   Copyright (C) 2011-2013 P. M. Sutter
 #

python_tools/void_python_tools/backend/__init__.py

@@ -1,5 +1,5 @@
 #+
-#   VIDE -- Void IDEntification pipeline -- ./python_tools/void_python_tools/backend/__init__.py
+#   VIDE -- Void IDentification and Examination -- ./python_tools/void_python_tools/backend/__init__.py
 #   Copyright (C) 2010-2013 Guilhem Lavaux
 #   Copyright (C) 2011-2013 P. M. Sutter
 #

python_tools/void_python_tools/backend/classes.py

@@ -1,5 +1,5 @@
 #+
-#   VIDE -- Void IDEntification pipeline -- ./python_tools/void_python_tools/backend/classes.py
+#   VIDE -- Void IDentification and Examination -- ./python_tools/void_python_tools/backend/classes.py
 #   Copyright (C) 2010-2013 Guilhem Lavaux
 #   Copyright (C) 2011-2013 P. M. Sutter
 #
@@ -58,7 +58,7 @@ class Sample:
   dataType = "observation"
   dataFormat = "sdss"
   dataFile = "lss.dr72dim.dat"
-  dataUNit = 1
+  dataUnit = 1
   fullName = "lss.dr72dim.dat"
   nickName = "dim"
   zobovDir = ""
@@ -72,11 +72,13 @@ class Sample:
   minVoidRadius = 5
   fakeDensity = 0.01
   profileBinSize = 2 # Mpc
+  autoNumInStack = -1 # set to >0 to automatically generate stacks of size N
   volumeLimited = True
   includeInHubble = True
   partOfCombo  = False
   isCombo = False
   useLCDM = False # if True, convert population to comoving coordinates
+  
   comboList = []
 
   # applies to simulations only
@@ -99,7 +101,7 @@ class Sample:
                numSubvolumes=1, mySubvolume=1, dataFormat="sdss",
                useLCDM=False,
                dataType="observation",
-               subsample=1.0, useLightCone=True):
+               subsample=1.0, useLightCone=True, autoNumInStack=-1):
     self.dataFile = dataFile
     self.fullName = fullName
     self.nickName = nickName
@@ -129,6 +131,7 @@ class Sample:
     self.useLightCone = useLightCone
     self.dataUnit = dataUnit
     self.useLCDM = useLCDM
+    self.autoNumInStack = autoNumInStack
 
     self.stacks = []
 

python_tools/void_python_tools/backend/launchers.py

@@ -1,5 +1,5 @@
 #+
-#   VIDE -- Void IDEntification pipeline -- ./python_tools/void_python_tools/backend/launchers.py
+#   VIDE -- Void IDentification and Examination -- ./python_tools/void_python_tools/backend/launchers.py
 #   Copyright (C) 2010-2013 Guilhem Lavaux
 #   Copyright (C) 2011-2013 P. M. Sutter
 #
@@ -35,6 +35,7 @@ import sys
 from   pylab import figure
 from   netCDF4 import Dataset
 from void_python_tools.backend.classes import *
+import pickle
 import void_python_tools.apTools as vp
 
 NetCDFFile = Dataset
@@ -261,7 +262,26 @@ def launchGenerate(sample, binPath, workDir=None, inputDataDir=None,
  
   meanSep = (1.*numTracers/boxVol)**(-1/3.) 
 
-  fp = open(zobovDir+"/sample_info.txt", 'a')
+  # save this sample's information
+  with open(zobovDir+"/sample_info.dat", 'w') as output:
+    pickle.dump(sample, output, pickle.HIGHEST_PROTOCOL)
+
+  fp = open(zobovDir+"/sample_info.txt", 'w')
+  fp.write("Sample name: %s\n" % sample.fullName)
+  fp.write("Sample nickname: %s\n" % sample.nickName)
+  fp.write("Data type: %s\n" % sample.dataType)
+  fp.write("Redshift range: %f - %f\n" %(sample.zBoundary[0],sample.zBoundary[1]))
+  if (sample.dataType == "simulation"):
+    fp.write("Particles placed on lightcone: %g\n" % sample.useLightCone)
+    fp.write("Peculiar velocities included: %g\n" % sample.usePecVel)
+    if (len(sample.subsample) == 1):
+      fp.write("Additional subsampling fraction: %s\n" % sample.subsample)
+    else:
+      fp.write("Additional subsampling fraction: %s\n" % sample.subsample[-1])
+    fp.write("Simulation box length (Mpc/h): %g\n" % sample.boxLen)
+    fp.write("Simulation Omega_M: %g\n" % sample.omegaM)
+    fp.write("Number of simulation subvolumes: %s\n" % sample.numSubvolumes)
+    fp.write("My subvolume index: %s\n" % sample.mySubvolume)
   fp.write("Estimated volume (cubic Mpc/h): %g\n" % boxVol)
   fp.write("Number of real (non-boundary) tracers: %d\n" % numTracers)
   fp.write("Total number of tracers: %d\n" % numTotal)
@@ -310,8 +330,9 @@ def launchZobov(sample, binPath, zobovDir=None, logDir=None, continueRun=None,
 
     cmd = "./%s >> %s 2>&1" % (vozScript, logFile)
     os.system(cmd)
+#cmd = "%s/../c_tools/zobov2/jozov2/jozov2 %s %s %s %s %s %g %s >> %s 2>&1" % \
 
-    cmd = "%s/../c_tools/zobov2/jozov2/jozov2 %s %s %s %s %s %g %s >> %s 2>&1" % \
+    cmd = "%s/jozov %s %s %s %s %s %g %s >> %s 2>&1" % \
           (binPath, \
            zobovDir+"/adj_"+sampleName+".dat", \
            zobovDir+"/vol_"+sampleName+".dat", \
@@ -455,8 +476,8 @@ def launchVoidOverlap(sample1, sample2, sample1Dir, sample2Dir,
            str(sampleName2)+".par"
     cmd += " --centerFile2=" + sample2Dir + \
            "/trimmed_nodencut_barycenters_"+thisDataPortion+"_"+str(sampleName2)+".out"
-    cmd += " --shapeFile2=" + sample1Dir + \
+    cmd += " --shapeFile2=" + sample2Dir + \
-           "/trimmed_nodencut_shapes_"+thisDataPortion+"_"+str(sampleName1)+".out"
+           "/trimmed_nodencut_shapes_"+thisDataPortion+"_"+str(sampleName2)+".out"
     cmd += " --zoneFile2=" + sample2Dir+"/voidZone_" + \
            str(sampleName2)+".dat"
     cmd += " --zonePartFile2=" + sample2Dir+"/voidPart_" + \

python_tools/void_python_tools/plotting/__init__.py

@@ -1,5 +1,5 @@
 #+
-#   VIDE -- Void IDEntification pipeline -- ./python_tools/void_python_tools/plotting/__init__.py
+#   VIDE -- Void IDentification and Examination -- ./python_tools/void_python_tools/plotting/__init__.py
 #   Copyright (C) 2010-2013 Guilhem Lavaux
 #   Copyright (C) 2011-2013 P. M. Sutter
 #

python_tools/void_python_tools/plotting/plotDefs.py

@@ -1,5 +1,5 @@
 #+
-#   VIDE -- Void IDEntification pipeline -- ./python_tools/void_python_tools/plotting/plotDefs.py
+#   VIDE -- Void IDentification and Examination -- ./python_tools/void_python_tools/plotting/plotDefs.py
 #   Copyright (C) 2010-2013 Guilhem Lavaux
 #   Copyright (C) 2011-2013 P. M. Sutter
 #

python_tools/void_python_tools/plotting/plotTools.py

@@ -1,5 +1,5 @@
 #+
-#   VIDE -- Void IDEntification pipeline -- ./python_tools/void_python_tools/plotting/plotTools.py
+#   VIDE -- Void IDentification and Examination -- ./python_tools/void_python_tools/plotting/plotTools.py
 #   Copyright (C) 2010-2013 Guilhem Lavaux
 #   Copyright (C) 2011-2013 P. M. Sutter
 #

python_tools/void_python_tools/xcor/__init__.py

@@ -1,5 +1,5 @@
 #+
-#   VIDE -- Void IDEntification pipeline -- ./python_tools/void_python_tools/plotting/__init__.py
+#   VIDE -- Void IDentification and Examination -- ./python_tools/void_python_tools/plotting/__init__.py
 #   Copyright (C) 2010-2013 Guilhem Lavaux
 #   Copyright (C) 2011-2013 P. M. Sutter
 #

zobov/vozinit.c

@@ -22,7 +22,8 @@ int main(int argc, char *argv[]) {
   int p; 
   int nvp, nvpall, nvpbuf, nvpmin, nvpmax, nvpbufmin, nvpbufmax; /* yes, the insurance */
   float width, width2, totwidth, totwidth2, bf, s, g;
-  float border, boxsize;
+  float widthX, widthY, widthZ;
+  float border, boxsize, boxsizeX, boxsizeY, boxsizeZ;
   float c[3];
   int numGuards;
   int b[3];
@@ -34,12 +35,12 @@ int main(int argc, char *argv[]) {
     printf("arg1: position file\n");
     printf("arg2: buffer size (default 0.1)\n");
     printf("arg3: box size\n");
-    printf("arg4: number of divisions (default 2)\n");
+    printf("arg6: number of divisions (default 2)\n");
-    printf("arg5: suffix describing this run\n");
+    printf("arg7: suffix describing this run\n");
-    printf("arg6: number of parallel threads\n");
+    printf("arg8: number of parallel threads\n");
-    printf("arg7: location of voboz executables\n");
+    printf("arg9: location of voboz executables\n");
-    printf("arg8: output directory\n");
+    printf("arg10: output directory\n");
-    printf("arg9: index of mock galaxies\n\n");
+    printf("arg11: index of mock galaxies\n\n");
     exit(0);
   }
   posfile = argv[1];
@@ -81,7 +82,8 @@ int main(int argc, char *argv[]) {
   np = posread(posfile,&rfloat,1./boxsize);
   /* Boxsize should be the range in r, yielding a range 0-1 */
 
-  width = 1./(float)numdiv;
+  width = boxsize/(float)numdiv;
+  //width = 1./(float)numdiv;
   width2 = 0.5*width;
   if (border > 0.) bf = border;
   else bf = 0.1;
@@ -171,12 +173,10 @@ int main(int argc, char *argv[]) {
   for (b[0]=0;b[0]<numdiv; b[0]++) {
    for (b[1] = 0; b[1] < numdiv; b[1]++) {
     for (b[2] = 0; b[2] < numdiv; b[2]++) {
-// TEST
+      fprintf(scr,"%s/voz1b1 %s %f %f %s %d %d %d %d %s&\n",
-      fprintf(scr,"%s/voz1b1 %s %f %f,%f,%f %s %d %d %d %d %s&\n",
         vobozPath,
-	      posfile,border,boxsize,boxsize,boxsize,suffix,numdiv,b[0],b[1],b[2], 
+	      posfile,border,boxsize,suffix,numdiv,b[0],b[1],b[2], 
         outDir);
-// END TEST
       p++;
       if ((p == numThreads)) { fprintf(scr, "wait\n"); p = 0; }
     }