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

c_tools/mock/generateMock.cpp

@@ -274,7 +274,7 @@ void selectBox(SimuData *simu, std::vector<long>& targets, generateMock_info& ar
         numAccepted++; 
       }
     }
-  cout << "Num accepted here = " << numAccepted <<  " / input = " << simu->NumPart << endl; 
+  cout << "SELECTBOX: Num accepted here = " << numAccepted <<  " / input = " << simu->NumPart << " (after resubsampling)" << endl; 
 }
 
 class PreselectParticles: public SimulationPreprocessor
@@ -385,7 +385,7 @@ void buildBox(SimuData *simu, long num_targets, long loaded,
     }
 }
 
-void saveBox(SimuData *&boxed, const std::string& outbox)
+void saveBox(SimuData *&boxed, const std::string& outbox, generateMock_info& args_info)
 {
   double *ranges = boxed->as<double>("ranges");
   NcFile f(outbox.c_str(), NcFile::Replace, 0, 0, NcFile::Netcdf4);
@@ -395,6 +395,11 @@ void saveBox(SimuData *&boxed, const std::string& outbox)
   int num_snapshots = *boxed->as<int>("num_snapshots");
   long *uniqueID = boxed->as<long>("uniqueID");
 
+  if (!f.is_valid())
+    {
+      cerr << "Could not create parameter file '" << outbox << "'. Aborting." << endl;
+      exit(1);
+    }
   f.add_att("range_x_min", ranges[0]);
   f.add_att("range_x_max", ranges[1]);
   f.add_att("range_y_min", ranges[2]);
@@ -403,6 +408,7 @@ void saveBox(SimuData *&boxed, const std::string& outbox)
   f.add_att("range_z_max", ranges[5]);
   f.add_att("mask_index", -1);
   f.add_att("is_observation", 0);
+  f.add_att("data_subsampling", args_info.subsample_arg);
 
   NcDim *NumPart_dim = f.add_dim("numpart_dim", boxed->NumPart);
   NcDim *NumSnap_dim = f.add_dim("numsnap_dim", num_snapshots);
@@ -446,6 +452,13 @@ void makeBoxFromParameter(SimuData *simu, SimuData* &boxed, generateMock_info& a
   boxed->time = simu->time;
   boxed->BoxSize = simu->BoxSize;
 
+  NcAtt *d_sub = f.get_att("data_subsampling");
+  if (d_sub == 0 || d_sub->as_double(0) != args_info.subsample_arg)
+   {
+     cerr << "Parameter file was not generated with the same simulation subsampling argument. Particles will be different. Stop here." << endl;
+     exit(1);
+   }
+
   NcVar *v_id = f.get_var("particle_ids");
   NcVar *v_snap = f.get_var("snapshot_split");
   long *edges1;
@@ -710,7 +723,7 @@ int main(int argc, char **argv)
       delete[] efac;
     }
 
-  saveBox(simuOut, args_info.outputParameter_arg);
+  saveBox(simuOut, args_info.outputParameter_arg, args_info);
   generateOutput(simuOut, args_info.axis_arg, 
                  args_info.output_arg);
   delete preselector;

c_tools/mock/loaders/sdf_loader.cpp

@@ -190,7 +190,7 @@ public:
     if (load_flags & (NEED_POSITION | NEED_VELOCITY))
       rescaleParticles(d, d->Hubble*1e-5, one_kpc/one_Gyr);
 
-//    enforceBoxSize(d);
+    enforceBoxSize(d);
     applyTransformations(d);
     basicPreprocessing(d, preproc);
 

external/external_build.cmake

@@ -234,6 +234,7 @@ ExternalProject_Add(cosmotool
 	-DGSLCBLAS_LIBRARY=${GSLCBLAS_LIBRARY}
 	-DNETCDF_LIBRARY=${NETCDF_LIBRARY}
 	-DNETCDFCPP_LIBRARY=${NETCDFCPP_LIBRARY}
+        -DENABLE_SHARP=OFF
 )
 SET(COSMOTOOL_LIBRARY ${CMAKE_BINARY_DIR}/ext_build/cosmotool/lib/libCosmoTool.a)
 set(COSMOTOOL_INCLUDE_PATH ${CMAKE_BINARY_DIR}/ext_build/cosmotool/include)

python_tools/void_python_tools/backend/launchers.py

@@ -163,6 +163,8 @@ def launchGenerate(sample, binPath, workDir=None, inputDataDir=None,
         dataFileLine = "gadget " + datafile
       elif sample.dataFormat == "sdf":
         dataFileLine = "sdf " + datafile
+      else:
+        raise ValueError("unknown dataFormat '%s'" % sample.dataFormat)
     
       iX = float(sample.mySubvolume[0])
       iY = float(sample.mySubvolume[1])

zobov/jozov.c

@@ -85,7 +85,7 @@ int main(int argc,char **argv) {
     printf("Bad density threshold.\n");
     exit(0);
   }
-  if (sscanf(argv[7],"%f",&mockIndex) == 0) {
+  if (sscanf(argv[7],"%d",&mockIndex) == 0) {
     printf("Bad mock galaxy index.\n");
     exit(0);
   }
@@ -108,29 +108,29 @@ int main(int argc,char **argv) {
   p = (PARTICLE *)malloc(np*sizeof(PARTICLE));
   /* Adjacencies*/
   for (i=0;i<np;i++) {
-    fread(&p[i].nadj,1,sizeof(int),adj); 
+    fread(&p[i].nadj,1,sizeof(pid_t),adj); 
     /* The number of adjacencies per particle */
     if (p[i].nadj > 0)
-      p[i].adj = (int *)malloc(p[i].nadj*sizeof(int));
+      p[i].adj = (pid_t *)malloc(p[i].nadj*sizeof(pid_t));
     else p[i].adj = 0;
     p[i].ncnt = 0; /* Temporarily, it's an adj counter */
   }
   for (i=0;i<np;i++) {
-    fread(&nin,1,sizeof(int),adj);
+    fread(&nin,1,sizeof(pid_t),adj);
     if (nin > 0)
       for (k=0;k<nin;k++) {
-	fread(&j,1,sizeof(int),adj);
+	fread(&j,1,sizeof(pid_t),adj);
 	if (j < np) {
 	  /* Set both halves of the pair */
 	assert(i < j);
           if (p[i].ncnt == p[i].nadj)
             {
-		p[i].adj = (int *)realloc(p[i].adj, (p[i].nadj+1)*sizeof(int));
+		p[i].adj = (pid_t *)realloc(p[i].adj, (p[i].nadj+1)*sizeof(pid_t));
                 p[i].nadj++;
             }
           if (p[j].ncnt == p[j].nadj)
             {
-              p[j].adj = (int *)realloc(p[j].adj, (p[j].nadj+1)*sizeof(int));
+              p[j].adj = (pid_t *)realloc(p[j].adj, (p[j].nadj+1)*sizeof(pid_t));
               p[j].nadj++;
             }
 	  p[i].adj[p[i].ncnt] = j;
@@ -144,13 +144,13 @@ int main(int argc,char **argv) {
   fclose(adj);
 
   /* Check that we got all the pairs */
-//  adj = fopen(adjfile, "r");
+  /*  adj = fopen(adjfile, "r");
-//  fread(&np,1, sizeof(int),adj);
+      fread(&np,1, sizeof(int),adj);*/
   for (i=0;i<np;i++) {
-//    fread(&nin,1,sizeof(int),adj); /* actually nadj */
+    /*    fread(&nin,1,sizeof(int),adj); /* actually nadj */
     // PMS
     if (p[i].ncnt != p[i].nadj && i < mockIndex) {
-    //if (p[i].ncnt != p[i].nadj) {
+      /*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);
@@ -185,9 +185,9 @@ int main(int argc,char **argv) {
   }
   fclose(vol);
 
-  jumped = (int *)malloc(np*sizeof(int));  
+  jumped = (pid_t *)malloc(np*sizeof(pid_t));  
-  jumper = (int *)malloc(np*sizeof(int));
+  jumper = (pid_t *)malloc(np*sizeof(pid_t));
-  numinh = (int *)malloc(np*sizeof(int));
+  numinh = (pid_t *)malloc(np*sizeof(pid_t));
 
   /* find jumper */
   for (i = 0; i < np; i++) {
@@ -252,7 +252,7 @@ int main(int argc,char **argv) {
     }
   
   for (h=0;h<nzones;h++) {
-    zt[h].adj = (int *)malloc(zt[h].nadj*sizeof(int));
+    zt[h].adj = (pid_t *)malloc(zt[h].nadj*sizeof(pid_t));
     if (zt[h].adj == NULL) {
       printf("Unable to allocate %d adj's of zone %d\n",zt[h].nadj,h);
       exit(0);
@@ -313,7 +313,7 @@ int main(int argc,char **argv) {
   for (h=0;h<nzones;h++) {
     /*printf("%d ",zt[h].nadj);*/
     z[h].nadj = zt[h].nadj;
-    z[h].adj = (int *)malloc(zt[h].nadj*sizeof(int));
+    z[h].adj = (pid_t *)malloc(zt[h].nadj*sizeof(pid_t));
     z[h].slv = (float *)malloc(zt[h].nadj*sizeof(float));
     for (za = 0; za<zt[h].nadj; za++) {
       z[h].adj[za] = zt[h].adj[za];
@@ -326,12 +326,12 @@ int main(int argc,char **argv) {
   free(zt);
   free(numinh);
 
-  m = (int **)malloc(nzones*sizeof(int *));
+  m = (pid_t **)malloc(nzones*sizeof(pid_t *));
   /* Not in the zone struct since it'll be freed up (contiguously, we hope)
      soon */
-  nm = (int *)malloc(nzones*sizeof(int));
+  nm = (pid_t *)malloc(nzones*sizeof(pid_t));
   for (h=0; h<nzones; h++) {
-    m[h] = (int *)malloc(z[h].np*sizeof(int));
+    m[h] = (pid_t *)malloc(z[h].np*sizeof(pid_t));
     nm[h] = 0;
     z[h].vol = 0.;
   }
@@ -354,14 +354,14 @@ int main(int argc,char **argv) {
     printf("Problem opening zonefile %s.\n\n",zonfile);
     exit(0);
   }
-  fwrite(&np,1,4,zon);
+  fwrite(&np,1,sizeof(pid_t),zon);
-  fwrite(&nzones,1,4,zon);
+  fwrite(&nzones,1,sizeof(int),zon);
   for (h=0; h<nzones; h++) {
 // PMS
   //printf("%d %d %d", &(z[h].np), m[h], z[h].np);
 // END PMS
-    fwrite(&(z[h].np),1,4,zon);
+    fwrite(&(z[h].np),1,sizeof(pid_t),zon);
-    fwrite(m[h],z[h].np,4,zon);
+    fwrite(m[h],z[h].np,sizeof(pid_t),zon);
     free(m[h]);
   }
   free(m);
@@ -394,7 +394,7 @@ int main(int argc,char **argv) {
     printf("Problem opening zonefile %s.\n\n",zonfile2);
     exit(0);
   }
-  fwrite(&nzones,1,4,zon2);
+  fwrite(&nzones,1,sizeof(int),zon2);
 
   for (h = 0; h<nzones; h++) {
     nhlcount = 0;
@@ -532,8 +532,8 @@ int main(int argc,char **argv) {
 
     z[h].nhl = nhl;
 
-    fwrite(&nhl,1,4,zon2);
+    fwrite(&nhl,1,sizeof(int),zon2);
-    fwrite(zonelist,nhl,4,zon2);
+    fwrite(zonelist,nhl,sizeof(int),zon2);
   }
   fclose(zon2);
 

zobov/voz.h

@@ -3,7 +3,9 @@
 ##define NGUARD 42 /*Actually, the number of SPACES between guard points
 		    in each dim */
 
+typedef int pid_t;
+
 typedef struct Partadj {
-  int nadj;
+  pid_t nadj;
-  int *adj;
+  pid_t *adj;
 } PARTADJ;

zobov/voz1b1.c

@@ -12,7 +12,7 @@ int posread(char *posfile, float ***p, float fact);
 
 int main(int argc, char *argv[]) {
   int exitcode;
-  int i, j, np;
+  pid_t i, j, np;
   float **r;
   coordT rtemp[3], *parts;
   coordT deladjs[3*MAXVERVER], points[3*MAXVERVER];
@@ -22,11 +22,12 @@ int main(int argc, char *argv[]) {
   PARTADJ *adjs;
   float *vols;
   float predict, xmin,xmax,ymin,ymax,zmin,zmax;
-  int *orig;
+  pid_t *orig;
   
   int isitinbuf;
   char isitinmain, d;
-  int numdiv, nvp, nvpall, nvpbuf;
+  int numdiv;
+  pid_t nvp, nvpall, nvpbuf;
   float width, width2, totwidth, totwidth2, bf, s, g;
   float border, boxsize;
   float c[3];
@@ -142,7 +143,7 @@ int main(int argc, char *argv[]) {
 					points */
 
   parts = (coordT *)malloc(3*nvpbuf*sizeof(coordT));
-  orig = (int *)malloc(nvpbuf*sizeof(int));
+  orig = (pid_t *)malloc(nvpbuf*sizeof(pid_t));
 
   if (parts == NULL) {
     printf("Unable to allocate parts\n");
@@ -182,15 +183,16 @@ int main(int argc, char *argv[]) {
   nvpbuf = nvp;
   for (i=0; i<np; i++) {
     isitinbuf = 1;
+    isitinmain = 1;
+
     DL {
       rtemp[d] = r[i][d] - c[d];
       if (rtemp[d] > 0.5) rtemp[d] --;
       if (rtemp[d] < -0.5) rtemp[d] ++;
       isitinbuf = isitinbuf && (fabs(rtemp[d])<totwidth2);
+      isitinmain = isitinmain && (fabs(rtemp[d]) <= width2);
     }
-    if ((isitinbuf > 0) &&
+    if (isitinbuf && !isitinmain) {
-	((fabs(rtemp[0])>width2)||(fabs(rtemp[1])>width2)||(fabs(rtemp[2])>width2))) {
-      
       /*printf("%3.3f ",sqrt(rtemp[0]*rtemp[0] + rtemp[1]*rtemp[1] +
 	rtemp[2]*rtemp[2]));
 	printf("|%2.2f,%2.2f,%2.2f,%f,%f",r[i][0],r[i][1],r[i][2],width2,totwidth2);*/
@@ -323,14 +325,14 @@ int main(int argc, char *argv[]) {
   printf("nvp = %d\n",nvp);
 
   /* Tell us where the original particles were */
-  fwrite(orig,sizeof(int),nvp,out);
+  fwrite(orig,sizeof(pid_t),nvp,out);
   /* Volumes*/
   fwrite(vols,sizeof(float),nvp,out);
   /* Adjacencies */
   for (i=0;i<nvp;i++) {
-    fwrite(&(adjs[i].nadj),1,sizeof(int),out);
+    fwrite(&(adjs[i].nadj),1,sizeof(pid_t),out);
     if (adjs[i].nadj > 0)
-      fwrite(adjs[i].adj,adjs[i].nadj,sizeof(int),out);
+      fwrite(adjs[i].adj,adjs[i].nadj,sizeof(pid_t),out);
     else printf("0");
   }
   fclose(out);

zobov/voztie.c

@@ -14,10 +14,12 @@ int main(int argc, char *argv[]) {
 
   int numdiv,np,np2,na;
 
-  int i,j,k,p,nout;
+  pid_t i,j,k,p,nout;
-  int nvp,npnotdone,nvpmax, nvpsum, *orig;
+  pid_t nvp,npnotdone,nvpmax, nvpsum, *orig;
   double avgnadj, avgvol;
 
+  int numRemoved = 0;
+  
   // PMS
   int mockIndex;
   // END PMS
@@ -87,7 +89,7 @@ int main(int argc, char *argv[]) {
   if (adjs == NULL) printf("Couldn't allocate adjs.\n");
   vols = (float *)malloc(np*sizeof(float));
   if (vols == NULL) printf("Couldn't allocate vols.\n");
-  orig = (int *)malloc(nvpmax*sizeof(int));
+  orig = (pid_t *)malloc(nvpmax*sizeof(pid_t));
   if (orig == NULL) printf("Couldn't allocate orig.\n");
   if ((cnt_adj==NULL) || (vols == NULL) || (orig == NULL) || (adjs == NULL)) {
     printf("Not enough memory to allocate. Exiting.\n");
@@ -96,6 +98,7 @@ int main(int argc, char *argv[]) {
   for (p=0;p<np;p++)
     vols[p] = -1.;
 
+  nvpsum = 0;
   for (i = 0; i < numdiv; i++) {
    for (j = 0; j < numdiv; j++) {
     for (k = 0; k < numdiv; k++) {
@@ -105,13 +108,13 @@ int main(int argc, char *argv[]) {
 	printf("Unable to open file %s.\n\n",partfile);
 	exit(0);
       }
-      fread(&np2,1,sizeof(int),part);
+      fread(&np2,1,sizeof(pid_t),part);
-      fread(&nvp,1,sizeof(int),part);
+      fread(&nvp,1,sizeof(pid_t),part);
       /*printf("nvp = %d\n",nvp);fflush(stdout);*/
 
       nvpsum += nvp;
 
-      fread(orig,nvp,sizeof(int),part);
+      fread(orig,nvp,sizeof(pid_t),part);
       for (p=0;p<nvp;p++) {
 	fread(&volstemp,1,sizeof(float),part);
 	if (vols[orig[p]] > -1.)
@@ -131,12 +134,12 @@ int main(int argc, char *argv[]) {
 	fread(&na,1,sizeof(int),part);
 	if (na > 0) {
 	  adjs[orig[p]].nadj = na;
-	  adjs[orig[p]].adj = (int *)malloc(na*sizeof(int));
+	  adjs[orig[p]].adj = (pid_t *)malloc(na*sizeof(pid_t));
 	  if (adjs[orig[p]].adj == NULL) {
 	    printf("Couldn't allocate adjs[orig[%d]].adj.\n",p);
 	    exit(0);
 	  }
-	  fread(adjs[orig[p]].adj,na,sizeof(int),part);
+	  fread(adjs[orig[p]].adj,na,sizeof(pid_t),part);
 	} else {
 	  printf("0"); fflush(stdout);
 	}
@@ -157,8 +160,6 @@ int main(int argc, char *argv[]) {
     adjs[i].nadj = 0;
   }
   
-  int numRemoved = 0;
-  
     // unlink particles adjacent to mock galaxies
     for (i = 0; i < mockIndex; i++) {
       for (j = 0; j < adjs[i].nadj; j++) {
@@ -217,7 +218,7 @@ printf("\n");
     avgvol += (double)(vols[p]);
   }
   if (npnotdone > 0)
-    printf("%d particles not done!\n");
+    printf("%d particles not done!\n", npnotdone);
   printf("%d particles done more than once.\n",nvpsum-np);
   avgnadj /= (double)np;
   avgvol /= (double)np;
@@ -272,9 +273,9 @@ printf("\n");
       for (j=0;j<adjs[i].nadj; j++) if (adjs[i].adj[j] > i) nout++;
       fwrite(&nout,1,sizeof(int),adj);      
       for (j=0;j<adjs[i].nadj; j++) {
-        int id = adjs[i].adj[j];
+        pid_t id = adjs[i].adj[j];
 	if (id > i) 
-	  fwrite(&(adjs[i].adj[j]),1,sizeof(int),adj);
+	  fwrite(&id,1,sizeof(pid_t),adj);
       }
     }