many bug fixes from the previous update; new changes appear to work now

c_tools/libzobov/contour_pixels.cpp

@@ -54,3 +54,33 @@ void computeContourPixels(Healpix_Map<float>& m, vector<int>& contour)
       write_Healpix_map_to_fits(h, contour_map, planckType<int>());
     }
 }
+
+void computeMaskPixels(Healpix_Map<float>& m, vector<int>& contour)
+{
+  for (int p = 0; p < m.Npix(); p++)
+    {
+
+    if (m[p]>0)
+      {
+        contour.push_back(p);
+        // This is boundary go to next pixel
+      }
+    }
+
+  if (DEBUG)
+    {
+      Healpix_Map<int> contour_map;
+
+      contour_map.SetNside(m.Nside(), RING);
+      contour_map.fill(0);
+      for (int p = 0; p < contour.size(); p++)
+  {
+    contour_map[contour[p]]=1;
+  }
+
+      fitshandle h;
+      h.create("!mask_map.fits");
+      write_Healpix_map_to_fits(h, contour_map, planckType<int>());
+    }
+}
+

c_tools/libzobov/contour_pixels.hpp

@@ -7,5 +7,6 @@
 
 void computeContourPixels(Healpix_Map<float>& map, std::vector<int>& contour);
 void computeFilledPixels(Healpix_Map<float>& map, std::vector<int>& contour);
+void computeMaskPixels(Healpix_Map<float>& map, std::vector<int>& contour);
 
 #endif

c_tools/mock/generateFromCatalog.cpp

@@ -295,10 +295,10 @@ void generateSurfaceMask(generateFromCatalog_info& args ,
 
   int nPart = 100;
 // TEST
-  for (int iDir = 0; iDir < 0; iDir++) {
+  //for (int iDir = 0; iDir < 0; iDir++) {
-  for (int iFace = 0; iFace < 0; iFace++) {
+  //for (int iFace = 0; iFace < 0; iFace++) {
-  //for (int iDir = 0; iDir < 3; iDir++) {
+  for (int iDir = 0; iDir < 3; iDir++) {
-  //for (int iFace = 0; iFace < 2; iFace++) {
+  for (int iFace = 0; iFace < 2; iFace++) {
 
     int iy = (iDir + 1) % 3;
     int iz = (iDir + 2) % 3;
@@ -483,6 +483,7 @@ void saveForZobov(ParticleData& pdata, const string& fname, const string& paramn
 
   //delete[] expansion_fac;
 
+/*
   FILE *infoFile = fopen("sample_info.txt", "w");
   fprintf(infoFile, "x_min = %f\n", -Lmax/100.);  
   fprintf(infoFile, "x_max = %f\n", Lmax/100.);
@@ -493,7 +494,7 @@ void saveForZobov(ParticleData& pdata, const string& fname, const string& paramn
   fprintf(infoFile, "mask_index = %d\n", pdata.mask_index);
   fprintf(infoFile, "total_particles = %d\n", pdata.pos.size());
   fclose(infoFile);
-
+*/
 
 }
 
@@ -545,6 +546,7 @@ int main(int argc, char **argv)
   mask.Import(o_mask);
 
   computeContourPixels(mask,pixel_list);
+  computeMaskPixels(mask,full_mask_list);
 
   // We compute a cube holding all the galaxies + the survey surface mask
 

c_tools/mock/generateMock.cpp

@@ -505,6 +505,7 @@ void makeBox(SimuData *simu, double *efac, SimuData *&boxed, generateMock_info&
   delete[] expansion_fac;
 
 
+/*
   FILE *fp = fopen("sample_info.txt", "w");
   fprintf(fp, "x_min = %f\n", ranges[0][0]);
   fprintf(fp, "x_max = %f\n", ranges[0][1]);
@@ -515,6 +516,7 @@ void makeBox(SimuData *simu, double *efac, SimuData *&boxed, generateMock_info&
   fprintf(fp, "mask_index = -1\n");
   fprintf(fp, "total_particles = %d\n", boxed->NumPart);
   fclose(fp);
+*/
 }
 
 void makeBoxFromParameter(SimuData *simu, double *efac, SimuData* &boxed, generateMock_info& args_info)

pipeline/generateCatalog.py

@@ -64,9 +64,23 @@ for sample in dataSampleList:
   # 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("Redshift range: %f - %f" %(sample.zBoundary[0], sample.zBoundary[1])
+  fp = open(zobovDir+"/sample_info.txt", 'w')
-  #fp.close()
+  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)
+    fp.write("Additional subsampling fraction: %g\n" % sample.subsample)
+    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: %g\n", sample.numSubvolumes)
+    fp.write("My subvolume index: %g\n", sample.mySubvolume)
+  fp.close()
 
 # ---------------------------------------------------------------------------
   if (startCatalogStage <= 1) and (endCatalogStage >= 1) and not sample.isCombo:

pipeline/prepareCatalogs.py

@@ -323,26 +323,28 @@ if (args.script or args.all) and dataFormat == "multidark":
   print " Doing halo scripts"
 
   for minHaloMass in minHaloMasses:
+    # estimate number of halos to get density
     dataFile = catalogDir+haloFileBase+fileNums[0]
     inFile = open(dataFile, 'r')
     numPart = 0
     for line in inFile: 
       line = line.split(',')
-      if numHaloMass == "none" or float(line[6]) > minHaloMass:
+      if minHaloMass == "none" or float(line[6]) > minHaloMass:
         numPart += 1
     inFile.close()
 
     minRadius = 2*int(np.ceil(lbox/numPart**(1./3.)))
   
     if dataFormat == "multidark":
-      setName = prefix+"halos_min"str(minHaloMass)
+      setName = prefix+"halos_min"+str(minHaloMass)
       writeScript(setName, "md.halos_min"+str(minHaloMass)+"_z", 
                 scriptDir, catalogDir, fileNums, 
                 redshifts, 
                 numSubvolumes, numSlices, False, lbox, minRadius, omegaM)
       writeScript(setName, "md.halos_min"+str(minHaloMass)+"_z", 
                 scriptDir, catalogDir, fileNums, 
-                numSlices, True, lbox, minRadius, omegaM)
+                redshifts, 
+                numSubvolumes, numSlices, True, lbox, minRadius, omegaM)
 
 if args.halos or args.all: 
   print " Doing halos"
@@ -355,9 +357,11 @@ if args.halos or args.all:
 
       dataFile = catalogDir+haloFileBase+fileNums[iRedshift]
       inFile = open(dataFile, 'r')
+      numPart = 0
       for line in inFile: 
         line = line.split(',')
-        if numHaloMass == "none" or float(line[6]) > minHaloMass:
+        if minHaloMass == "none" or float(line[6]) > minHaloMass:
+          numPart += 1
       inFile.close()
 
       sampleName = "md.halos_z"+redshift
@@ -370,18 +374,16 @@ if args.halos or args.all:
       outFile.write("%d\n" %(numPart))
 
       inFile = open(dataFile, 'r')
-      numKept = 0
+      for (iHalo,line) in enumerate(inFile):
-      for line in inFile:
-        if numHaloMass == "none" or float(line[6]) > minHaloMass:
-          numKept += 1
         line = line.split(',')
+        if minHaloMass == "none" or float(line[6]) > minHaloMass:
           x  = float(line[0])
           y  = float(line[1])
           z  = float(line[2])
           vz = float(line[5])
 
           # write to output file
-          outFile.write("%d %e %e %e %e\n" %(numKept,x,y,z,vz))
+          outFile.write("%d %e %e %e %e\n" %(iHalo,x,y,z,vz))
 
       inFile.close()
       outFile.close()

python_tools/void_python_tools/backend/launchers.py

@@ -83,7 +83,7 @@ def launchGenerate(sample, binPath, workDir=None, inputDataDir=None,
     if os.access("mask_index.txt", os.F_OK):
       os.system("mv %s %s" % ("mask_index.txt", zobovDir))
       os.system("mv %s %s" % ("total_particles.txt", zobovDir))
-      os.system("mv %s %s" % ("sample_info.txt", zobovDir))
+      #os.system("mv %s %s" % ("sample_info.txt", zobovDir))
 
     if os.access("galaxies.txt", os.F_OK):
       os.system("mv %s %s" % ("galaxies.txt", zobovDir))
@@ -160,7 +160,7 @@ def launchGenerate(sample, binPath, workDir=None, inputDataDir=None,
 
     if os.access("comoving_distance.txt", os.F_OK):
       os.system("mv %s %s" % ("comoving_distance.txt", zobovDir))
-      os.system("mv %s %s" % ("sample_info.txt", zobovDir))
+      #os.system("mv %s %s" % ("sample_info.txt", zobovDir))
 
     if os.access(parmFile, os.F_OK):
       os.unlink(parmFile)