more bug fixes for the minimum halo mass cuts...sigh

README

@@ -1,13 +1,10 @@
 After compiling, go to the pipeline directory.
 
-Edit the parameters at the top of prepareGadgetCatalog.py: decide
+Create a dataset parameter file. Look at datasets/multidark.py for 
-where to put outputs, how many redshifts to do, how many slices,
+an example. Describe the simulation, where to put outputs, how many 
-subdivisions, subsamples, etc. etc.
+redshift slices, subvolumes, etc. etc.
 
-Note that eventually prepareGadgetCatalog will be replaced by the more
+prepareCatalogs will produce a pipeline script for each
-general and flexible prepareCatalogs.
-
-prepareGadgetCatalogs will produce a pipeline script for each
 subsampling you choose. If you have multiple redshift particle files,
 and choose multiple slices and/or subdivisions, they will be packaged
 in the same pipeline script.
@@ -22,16 +19,10 @@ Check the logfiles for any error messages.
 See the README of the public void catalog for the format of the
 outputs.
 
-I'm also working on incorporating plotting into the pipeline script,
-so that you can immediately get some basic info about the voids.
-
 Please do not change the outputs of pruneVoids etc. without
 discussion, since further analysis relies on the current formats.
 
 If you're wondering why these scripts are rather complex, it's because
 it can also support A-P analysis, which is much more complicated :)
 
-We can talk about ways to incorporate your analysis into the pipline
-and to have your tools under this umbrella.
-
 Good luck!

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;

c_tools/mock/generateMock.cpp

@@ -179,14 +179,18 @@ SimuData *doLoadMultidark(const char *multidarkname)
     outd->Pos[k] = new float[outd->NumPart];
   outd->Vel[2] = new float[outd->NumPart];
   outd->Id = new int[outd->NumPart];
+  outd->uniqueID = new float[outd->NumPart];
 
   cout << "loading multidark particles" << endl;
   actualNumPart = 0;
 	for (int i = 0; i < outd->NumPart; i++) {
-    fscanf(fp, "%d %d %f %f %f\n", &outd->Id[i], 
+    fscanf(fp, "%d %f %f %f %f\n", &outd->Id[i], 
                                 &outd->Pos[0][i], &outd->Pos[1][i], 
                                 &outd->Pos[2][i], &outd->Vel[2][i]);
 
+    outd->uniqueID[i] = 1.0;
+    //outd->uniqueID[i] = 1.0 * outd->Id[i];
+
     if (outd->Id[i] == -99 && 
         outd->Pos[0][i] == -99 && outd->Pos[1][i] == -99 && 
         outd->Pos[2][i] == -99 && outd->Vel[2][i] == -99) {
@@ -368,7 +372,7 @@ void generateOutput(SimuData *data, int axis,
   f.beginCheckpoint();
   for (uint32_t i = 0; i < data->NumPart; i++)
     {
-      f.writeReal32(data->Id[i]);
+      f.writeReal32(data->Pos[x0][i]);
     }
   f.endCheckpoint();
 
@@ -376,7 +380,7 @@ void generateOutput(SimuData *data, int axis,
   f.beginCheckpoint();
   for (uint32_t i = 0; i < data->NumPart; i++)
     {
-      f.writeReal32(data->Id[i]);
+      f.writeReal32(data->Pos[x1][i]);
     }
   f.endCheckpoint();
 
@@ -384,7 +388,7 @@ void generateOutput(SimuData *data, int axis,
   f.beginCheckpoint();
   for (uint32_t i = 0; i < data->NumPart; i++)
     {
-      f.writeReal32(data->Id[i]);
+      f.writeReal32(data->Pos[x2][i]);
     }
   f.endCheckpoint();
 
@@ -392,11 +396,11 @@ void generateOutput(SimuData *data, int axis,
   f.beginCheckpoint();
   for (uint32_t i = 0; i < data->NumPart; i++)
     {
-      f.writeReal32(data->Id[i]);
+      //printf("HELLO %d %d\n", i, data->Id[i]);
+      //f.writeReal32(data->Id[i]);
+      f.writeReal32(data->uniqueID[i]);
     }
   f.endCheckpoint();
-
-
 }
 
 void makeBox(SimuData *simu, double *efac, SimuData *&boxed, generateMock_info& args_info)
@@ -456,6 +460,7 @@ void makeBox(SimuData *simu, double *efac, SimuData *&boxed, generateMock_info&
       boxed->Vel[j] = 0;
       mul[j] = 1.0/(ranges[j][1] - ranges[j][0]);
     }
+  boxed->uniqueID = new float[goodParticles];
 
   cout << "Rescaling factors = " << mul[0] << " " << mul[1] << " " << mul[2] << endl;
   boxed->NumPart = goodParticles;
@@ -476,6 +481,8 @@ void makeBox(SimuData *simu, double *efac, SimuData *&boxed, generateMock_info&
 	      assert(boxed->Pos[j][k] > 0);
 	      assert(boxed->Pos[j][k] < 1);
 	    }
+    boxed->uniqueID[k] = simu->uniqueID[i];
+
 	  particle_id[k] = i;
           expansion_fac[k] = efac[i];
 	  k++;

c_tools/stacking/pruneVoids.cpp

@@ -451,28 +451,29 @@ int main(int argc, char **argv) {
       //voids[iVoid].accepted = 0;
     }
  
+    if (voids[iVoid].centralDen > args_info.maxCentralDen_arg) {
+      voids[iVoid].accepted = -1;
+    }
+
     // toss out voids that are obviously wrong
     if (voids[iVoid].densCon > 1.e3) {
-      voids[iVoid].accepted = 0;
+      voids[iVoid].accepted = -4;
     }
 
     if (strcmp(args_info.dataPortion_arg, "edge")  == 0 &&
         tolerance*voids[iVoid].maxRadius < voids[iVoid].nearestMock) {
-      voids[iVoid].accepted = 0;
+      voids[iVoid].accepted = -3;
     }
 
     if (strcmp(args_info.dataPortion_arg, "central") == 0 && 
         tolerance*voids[iVoid].maxRadius > voids[iVoid].nearestMock) {
-      voids[iVoid].accepted = 0;
+      voids[iVoid].accepted = -3;
     }
 
     if (voids[iVoid].radius < args_info.rMin_arg) {
-      voids[iVoid].accepted = 0;
+      voids[iVoid].accepted = -2;
     }
 
-    if (voids[iVoid].centralDen > args_info.maxCentralDen_arg) {
-      voids[iVoid].accepted = -1;
-    }
   }
 
   numKept = 0;
@@ -559,7 +560,7 @@ int main(int argc, char **argv) {
   fprintf(fpInfo, "# center x,y,z (km/s), volume (normalized), radius (Mpc/h), redshift, volume (Mpc/h^3), void ID\n");
   for (iVoid = 0; iVoid < numVoids; iVoid++) {
 
-    if (voids[iVoid].accepted == 0) continue;
+    if (voids[iVoid].accepted < -1) continue;
 
      double outCenter[3];
      outCenter[0] = voids[iVoid].barycenter[0];

external/cosmotool/src/loadSimu.hpp

@@ -27,7 +27,7 @@ namespace CosmoTool
     float *uniqueID;
     int *type;
   public:
-    SimuData() : Id(0),NumPart(0),type(0), uniqueID(0)  { Pos[0]=Pos[1]=Pos[2]=0; Vel[0]=Vel[1]=Vel[2]=0; uniqueID=0}
+    SimuData() : Id(0),NumPart(0),type(0), uniqueID(0)  { Pos[0]=Pos[1]=Pos[2]=0; Vel[0]=Vel[1]=Vel[2]=0; uniqueID=0;}
     ~SimuData() 
     {
       for (int j = 0; j < 3; j++)

pipeline/generateCatalog.py

@@ -78,8 +78,8 @@ for sample in dataSampleList:
     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("Number of simulation subvolumes: %s\n" % sample.numSubvolumes)
-    fp.write("My subvolume index: %g\n", sample.mySubvolume)
+    fp.write("My subvolume index: %s\n" % sample.mySubvolume)
   fp.close()
 
 # ---------------------------------------------------------------------------

pipeline/prepareCatalogs.py

@@ -364,7 +364,7 @@ if args.halos or args.all:
           numPart += 1
       inFile.close()
 
-      sampleName = "md.halos_z"+redshift
+      sampleName = "md.halos_min"+str(minHaloMass)+"_z"+redshift
       outFile = open(catalogDir+"/"+sampleName+".dat", 'w')
 
       outFile.write("%f\n" %(lbox))
@@ -385,6 +385,7 @@ if args.halos or args.all:
           # write to output file
           outFile.write("%d %e %e %e %e\n" %(iHalo,x,y,z,vz))
 
+      outFile.write("-99 -99 -99 -99 -99\n")
       inFile.close()
       outFile.close()
 

plotting/datasetsToPlot.py

@@ -5,7 +5,7 @@ workDir = "/home/psutter2/workspace/Voids/"
 figDir  = "./figs"
 
 sampleDirList = [ "multidark/md_ss0.1_pv/sample_md_ss0.1_pv_z0.56_d00/",
-                  "multidark/md_ss01.0_pv/sample_md_ss1.0_pv_z0.56_d00/",
+                  #"multidark/md_ss01.0_pv/sample_md_ss1.0_pv_z0.56_d00/",
                   "multidark/md_halos_min1.23e13_pv/sample_md_halos_min1.23e13_pv_z0.56_d00/",
                   "random/ran_ss0.0004/sample_ran_ss0.0004_z0.56_d00/",
                   "random/ran_ss0.1/sample_ran_ss0.1_z0.56_d00/",

python_tools/void_python_tools/backend/launchers.py

@@ -55,7 +55,7 @@ def launchGenerate(sample, binPath, workDir=None, inputDataDir=None,
              sample.zBoundary[0], sample.zBoundary[1], sample.fakeDensity,
              useLCDMFlag)
 
-    parmFile = os.getcwd()+"/generate.par"
+    parmFile = os.getcwd()+"/generate_"+sample.fullName+".par"
 
     file(parmFile, mode="w").write(conf)
 
@@ -143,7 +143,7 @@ def launchGenerate(sample, binPath, workDir=None, inputDataDir=None,
              sample.zBoundaryMpc[0], sample.zBoundaryMpc[1],
              sample.subsample)
 
-    parmFile = os.getcwd()+"/generate.par"
+    parmFile = os.getcwd()+"/generate_"+sample.fullName+".par"
 
     file(parmFile, mode="w").write(conf)
 
@@ -405,7 +405,7 @@ def launchStack(sample, stack, binPath, thisDataPortion=None, logDir=None,
    zobovDir+"/boundaryDistances_"+thisDataPortion+"_"+sampleName+".out",
    rescaleFlag)
 
-  parmFile = os.getcwd()+"/stack.par"
+  parmFile = os.getcwd()+"/stack_"+sample.fullName+".par"
 
   fp = file(parmFile, mode="w")
   fp.write(conf)