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removed mock particle tracking, since that is no longer used

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This commit is contained in:
Paul M. Sutter 2025-04-21 16:23:25 -04:00
parent fc2d7157f4
commit d9efa15474
8 changed files with 71 additions and 173 deletions
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18
c_source/prep/prepObservation.cpp
View file

@ -64,9 +64,6 @@ struct ParticleData
vector<double> redshift; vector<double> redshift;
vector<double> catalogID; vector<double> catalogID;
vector<long> uniqueID; vector<long> uniqueID;
// PMS
int mask_index;
// END PMS
int edgeFlag = 0; int edgeFlag = 0;
vector<Position> pos; vector<Position> pos;
double box[3][2]; double box[3][2];
@ -263,12 +260,8 @@ void flagEdgeGalaxies(prepObservation_info& args ,
size_t nEval; size_t nEval;
//End Maubert - Needed for comobile distance in mock_sphere //End Maubert - Needed for comobile distance in mock_sphere
// TODO - REMOVE THIS
output_data.mask_index = output_data.id_gal.size();
// write a small text file with galaxy position (for diagnostic purposes) // write a small text file with galaxy position (for diagnostic purposes)
// TODO - remove this // TODO - remove this
FILE *fp; FILE *fp;
fp = fopen("galaxies.txt", "w"); fp = fopen("galaxies.txt", "w");
//for (int i = 0; i < output_data.id_gal.size(); i++) { //for (int i = 0; i < output_data.id_gal.size(); i++) {
@ -414,11 +407,9 @@ void saveForZobov(ParticleData& pdata, const string& fname,
fp.putAtt("range_y_max", ncDouble, Lmax/100.); fp.putAtt("range_y_max", ncDouble, Lmax/100.);
fp.putAtt("range_z_min", ncDouble, -Lmax/100.); fp.putAtt("range_z_min", ncDouble, -Lmax/100.);
fp.putAtt("range_z_max", ncDouble, Lmax/100.); fp.putAtt("range_z_max", ncDouble, Lmax/100.);
fp.putAtt("mask_index", ncInt, pdata.mask_index); // PMS fp.putAtt("is_observation", ncInt, 1);
fp.putAtt("is_observation", ncInt, 1); // PMS
int nOutputPart = pdata.mask_index; int nOutputPart = pdata.pos.size();
//int nOutputPart = pdata.pos.size();
NcDim NumPart_dim = fp.addDim("numpart_dim", nOutputPart); NcDim NumPart_dim = fp.addDim("numpart_dim", nOutputPart);
NcVar v = fp.addVar("particle_ids", ncInt, NumPart_dim); NcVar v = fp.addVar("particle_ids", ncInt, NumPart_dim);
@ -497,10 +488,7 @@ int main(int argc, char **argv)
saveForZobov(output_data, args_info.output_arg, args_info.params_arg); saveForZobov(output_data, args_info.output_arg, args_info.params_arg);
// PMS - TODO REMOVE THIS // PMS - TODO REMOVE THIS
FILE *fp = fopen("mask_index.txt", "w"); FILE *fp;
fprintf(fp, "%d", output_data.mask_index);
fclose(fp);
fp = fopen("total_particles.txt", "w"); fp = fopen("total_particles.txt", "w");
fprintf(fp, "%d", output_data.pos.size()); fprintf(fp, "%d", output_data.pos.size());
fclose(fp); fclose(fp);

56
c_source/pruning/pruneVoids.cpp
View file

@ -116,7 +116,7 @@ double expanFun (double z, void * p) {
void openFiles(string outputDir, string sampleName, void openFiles(string outputDir, string sampleName,
string prefix, string dataPortion, string prefix, string dataPortion,
int mockIndex, int numKept, int numPartTot, int numKept,
FILE** fpZobov, FILE** fpCenters, FILE** fpZobov, FILE** fpCenters,
FILE** fpCentersNoCut, FILE** fpCentersNoCut,
FILE** fpBarycenter, FILE** fpShapes, FILE** fpBarycenter, FILE** fpShapes,
@ -128,7 +128,7 @@ void closeFiles(FILE* fpZobov, FILE* fpCenters,
FILE* fpSkyPositions); FILE* fpSkyPositions);
void outputVoids(string outputDir, string sampleName, string prefix, void outputVoids(string outputDir, string sampleName, string prefix,
string dataPortion, int mockIndex, string dataPortion, int numPartTot,
vector<VOID> voids, vector<VOID> voids,
bool isObservation, double *boxLen, bool isObservation, double *boxLen,
bool doTrim, bool doCentralDenCut); bool doTrim, bool doCentralDenCut);
@ -187,7 +187,7 @@ int main(int argc, char **argv) {
int i, p, p2, numPartTot, numZonesTot, dummy, iVoid; int i, p, p2, numPartTot, numZonesTot, dummy, iVoid;
int numVoids, mockIndex; int numVoids;
double tolerance; double tolerance;
FILE *fp; FILE *fp;
PART *part, *voidPart, *flaggedPart; PART *part, *voidPart, *flaggedPart;
@ -202,7 +202,6 @@ int main(int argc, char **argv) {
double nearestEdge, redshift; double nearestEdge, redshift;
char line[500], junkStr[10]; char line[500], junkStr[10];
string outputDir, sampleName, dataPortion, prefix; string outputDir, sampleName, dataPortion, prefix;
int mask_index;
double ranges[3][2], boxLen[3], mul; double ranges[3][2], boxLen[3], mul;
double volNorm, radius; double volNorm, radius;
int clock1, clock2, clock3, clock4; int clock1, clock2, clock3, clock4;
@ -213,7 +212,6 @@ int main(int argc, char **argv) {
gsl_eigen_symmv_workspace *eigw = gsl_eigen_symmv_alloc(3); gsl_eigen_symmv_workspace *eigw = gsl_eigen_symmv_alloc(3);
numVoids = args.numVoids_arg; numVoids = args.numVoids_arg;
mockIndex = args.mockIndex_arg;
tolerance = args.tolerance_arg; tolerance = args.tolerance_arg;
clock1 = clock(); clock1 = clock();
@ -309,9 +307,6 @@ int main(int argc, char **argv) {
interval = 1.*(clock4 - clock3)/CLOCKS_PER_SEC; interval = 1.*(clock4 - clock3)/CLOCKS_PER_SEC;
printf(" Read %d particles (%.2f sec)...\n", numPartTot, interval); printf(" Read %d particles (%.2f sec)...\n", numPartTot, interval);
if (mockIndex == -1) mockIndex = numPartTot;
// read in desired voids // read in desired voids
clock3 = clock(); clock3 = clock();
printf(" Loading voids...\n"); printf(" Loading voids...\n");
@ -393,12 +388,8 @@ int main(int argc, char **argv) {
// and volumes // and volumes
printf(" Loading particle volumes...\n"); printf(" Loading particle volumes...\n");
fp = fopen(args.partVol_arg, "r"); fp = fopen(args.partVol_arg, "r");
fread(&mask_index, 1, 4, fp); fread(&numPartTot, 1, 4, fp);
if (mask_index != mockIndex) { for (p = 0; p < numPartTot; p++) {
printf("NON-MATCHING MOCK INDICES!? %d %d\n", mask_index, mockIndex);
exit(-1);
}
for (p = 0; p < mask_index; p++) {
fread(&temp[0], 1, 4, fp); fread(&temp[0], 1, 4, fp);
part[p].vol = temp[0]; part[p].vol = temp[0];
} }
@ -408,7 +399,7 @@ int main(int argc, char **argv) {
printf(" Loading particle edge flags...\n"); printf(" Loading particle edge flags...\n");
int numFlagged = 0; int numFlagged = 0;
fp = fopen(args.partEdge_arg, "r"); fp = fopen(args.partEdge_arg, "r");
for (p = 0; p < mask_index; p++) { for (p = 0; p < numPartTot; p++) {
fscanf(fp, "%d", &part[p].edgeFlag); fscanf(fp, "%d", &part[p].edgeFlag);
if (part[p].edgeFlag > 0) numFlagged++; if (part[p].edgeFlag > 0) numFlagged++;
} }
@ -417,7 +408,7 @@ int main(int argc, char **argv) {
// copy flagged galaxies to separate array for faster processing later // copy flagged galaxies to separate array for faster processing later
flaggedPart = (PART *) malloc(numFlagged * sizeof(PART)); flaggedPart = (PART *) malloc(numFlagged * sizeof(PART));
int iFlag = 0; int iFlag = 0;
for (p = 0; p < mask_index; p++) { for (p = 0; p < numPartTot; p++) {
if (part[p].edgeFlag > 0) { if (part[p].edgeFlag > 0) {
flaggedPart[iFlag] = part[p]; flaggedPart[iFlag] = part[p];
iFlag++; iFlag++;
@ -428,20 +419,20 @@ int main(int argc, char **argv) {
// and finally finally adjacencies // and finally finally adjacencies
printf(" Loading particle adjacencies...\n"); printf(" Loading particle adjacencies...\n");
fp = fopen(args.partAdj_arg, "r"); fp = fopen(args.partAdj_arg, "r");
fread(&mask_index, 1, 4, fp); fread(&numPartTot, 1, 4, fp);
if (mask_index != mockIndex) { if (numPartTot != numPartTot) {
printf("NON-MATCHING MOCK INDICES!? %d %d\n", mask_index, mockIndex); printf("NON-MATCHING MOCK INDICES!? %d %d\n", numPartTot, numPartTot);
exit(-1); exit(-1);
} }
int tempInt; int tempInt;
for (p = 0; p < mask_index; p++) { for (p = 0; p < numPartTot; p++) {
fread(&tempInt, 1, 4, fp); fread(&tempInt, 1, 4, fp);
part[p].nadj = tempInt; part[p].nadj = tempInt;
part[p].ncnt = 0; part[p].ncnt = 0;
if (part[p].nadj > 0) if (part[p].nadj > 0)
part[p].adj = (int *) malloc(part[p].nadj * sizeof(int)); part[p].adj = (int *) malloc(part[p].nadj * sizeof(int));
} }
for (p = 0; p < mask_index; p++) { for (p = 0; p < numPartTot; p++) {
fread(&tempInt, 1, 4, fp); fread(&tempInt, 1, 4, fp);
int nin = tempInt; int nin = tempInt;
if (nin > 0) { if (nin > 0) {
@ -452,7 +443,7 @@ int main(int argc, char **argv) {
// this bit has been readjusted just in case we are // this bit has been readjusted just in case we are
// accidentally still linking to mock particles // accidentally still linking to mock particles
//if (tempAdj < mask_index) { //if (tempAdj < numPartTot) {
assert(p < tempAdj); assert(p < tempAdj);
//if (part[p].ncnt == part[p].nadj) { //if (part[p].ncnt == part[p].nadj) {
// printf("OVERFLOW %d\n", p); // printf("OVERFLOW %d\n", p);
@ -461,7 +452,7 @@ int main(int argc, char **argv) {
//} else { //} else {
part[p].adj[part[p].ncnt] = tempAdj; part[p].adj[part[p].ncnt] = tempAdj;
part[p].ncnt++; part[p].ncnt++;
if (tempAdj < mask_index) { if (tempAdj < numPartTot) {
part[tempAdj].adj[part[tempAdj].ncnt] = p; part[tempAdj].adj[part[tempAdj].ncnt] = p;
part[tempAdj].ncnt++; part[tempAdj].ncnt++;
} }
@ -542,9 +533,8 @@ int main(int argc, char **argv) {
partID = zones2Parts[zoneID].partIDs[p]; partID = zones2Parts[zoneID].partIDs[p];
// something went haywire // something went haywire
if (partID > mask_index || if (part[partID].vol < 1.e-27 && part[partID].vol > 0.) {
(part[partID].vol < 1.e-27 && part[partID].vol > 0.)) { printf("BAD PART!? %d %d %e", partID, numPartTot, part[partID].vol);
printf("BAD PART!? %d %d %e", partID, mask_index, part[partID].vol);
exit(-1); exit(-1);
} }
@ -567,7 +557,7 @@ int main(int argc, char **argv) {
//printf("NORMAL!! %d %d %e\n", iVoid, partID, part[partID].vol); //printf("NORMAL!! %d %d %e\n", iVoid, partID, part[partID].vol);
} }
for (int iAdj = 0; iAdj < part[partID].ncnt; iAdj++) { for (int iAdj = 0; iAdj < part[partID].ncnt; iAdj++) {
if (part[partID].adj[iAdj] > mockIndex) { if (part[partID].adj[iAdj] > numPartTot) {
printf("CONTAMINATED!! %d %d %d\n", iVoid, partID, iAdj); printf("CONTAMINATED!! %d %d %d\n", iVoid, partID, iAdj);
} }
} }
@ -949,7 +939,7 @@ int main(int argc, char **argv) {
for (int i = 0; i < 2; i++) { for (int i = 0; i < 2; i++) {
dataPortion = dataPortions[i]; dataPortion = dataPortions[i];
outputVoids(outputDir, sampleName, prefix, dataPortion, outputVoids(outputDir, sampleName, prefix, dataPortion,
mockIndex, numPartTot,
voids, voids,
args.isObservation_flag, boxLen, true, true); args.isObservation_flag, boxLen, true, true);
} }
@ -959,7 +949,7 @@ int main(int argc, char **argv) {
for (int i = 0; i < 2; i++) { for (int i = 0; i < 2; i++) {
dataPortion = dataPortions[i]; dataPortion = dataPortions[i];
outputVoids(outputDir, sampleName, prefix, dataPortion, outputVoids(outputDir, sampleName, prefix, dataPortion,
mockIndex, numPartTot,
voids, voids,
args.isObservation_flag, boxLen, false, false); args.isObservation_flag, boxLen, false, false);
} }
@ -977,14 +967,14 @@ int main(int argc, char **argv) {
// ---------------------------------------------------------------------------- // ----------------------------------------------------------------------------
void openFiles(string outputDir, string sampleName, void openFiles(string outputDir, string sampleName,
string prefix, string dataPortion, string prefix, string dataPortion,
int mockIndex, int numKept, int numPartTot, int numKept,
FILE** fpZobov, FILE** fpCenters, FILE** fpZobov, FILE** fpCenters,
FILE** fpBarycenter, FILE** fpShapes, FILE** fpBarycenter, FILE** fpShapes,
FILE** fpExtra, FILE** fpExtra,
FILE** fpSkyPositions) { FILE** fpSkyPositions) {
*fpZobov = fopen((outputDir+"/"+prefix+"voidDesc_"+dataPortion+"_"+sampleName).c_str(), "w"); *fpZobov = fopen((outputDir+"/"+prefix+"voidDesc_"+dataPortion+"_"+sampleName).c_str(), "w");
fprintf(*fpZobov, "%d particles, %d voids.\n", mockIndex, numKept); fprintf(*fpZobov, "%d particles, %d voids.\n", numPartTot, numKept);
fprintf(*fpZobov, "Void# FileVoid# CoreParticle CoreDens ZoneVol Zone#Part Void#Zones VoidVol Void#Part VoidDensContrast VoidProb\n"); fprintf(*fpZobov, "Void# FileVoid# CoreParticle CoreDens ZoneVol Zone#Part Void#Zones VoidVol Void#Part VoidDensContrast VoidProb\n");
*fpBarycenter = fopen((outputDir+"/"+prefix+"macrocenters_"+dataPortion+"_"+sampleName).c_str(), "w"); *fpBarycenter = fopen((outputDir+"/"+prefix+"macrocenters_"+dataPortion+"_"+sampleName).c_str(), "w");
@ -1022,7 +1012,7 @@ void closeFiles(FILE* fpZobov, FILE* fpCenters,
// ---------------------------------------------------------------------------- // ----------------------------------------------------------------------------
void outputVoids(string outputDir, string sampleName, string prefix, void outputVoids(string outputDir, string sampleName, string prefix,
string dataPortion, int mockIndex, string dataPortion, int numPartTot,
vector<VOID> voids, vector<VOID> voids,
bool isObservation, double *boxLen, bool doTrim, bool isObservation, double *boxLen, bool doTrim,
bool doCentralDenCut) { bool doCentralDenCut) {
@ -1034,7 +1024,7 @@ void outputVoids(string outputDir, string sampleName, string prefix,
openFiles(outputDir, sampleName, prefix, dataPortion, openFiles(outputDir, sampleName, prefix, dataPortion,
mockIndex, voids.size(), numPartTot, voids.size(),
&fpZobov, &fpCenters, &fpBarycenter, &fpZobov, &fpCenters, &fpBarycenter,
&fpShapes, &fpExtra, &fpSkyPositions); &fpShapes, &fpExtra, &fpSkyPositions);

1
c_source/pruning/pruneVoids.ggo
View file

@ -19,7 +19,6 @@ option "partAdj" - "Adjacency file from ZOBOV" string required
option "partEdge" - "Boundary flag file" string required option "partEdge" - "Boundary flag file" string required
option "zone2Part" - "Particle file from ZOBOV" string required option "zone2Part" - "Particle file from ZOBOV" string required
option "mockIndex" - "Beginning index of mock particles" int required
option "numVoids" - "Number of voids" int required option "numVoids" - "Number of voids" int required

16
c_source/zobov/jozov.c
View file

@ -61,8 +61,6 @@ int main(int argc,char **argv) {
double *sorter, e1,maxdenscontrast; double *sorter, e1,maxdenscontrast;
int *iord; int *iord;
int mockIndex;
e1 = exp(1.)-1.; e1 = exp(1.)-1.;
if (argc != 8) { if (argc != 8) {
@ -73,7 +71,6 @@ int main(int argc,char **argv) {
printf("arg4: output file containing zones in each void\n"); printf("arg4: output file containing zones in each void\n");
printf("arg5: output text file\n"); printf("arg5: output text file\n");
printf("arg6: Density threshold (0 for no threshold)\n"); printf("arg6: Density threshold (0 for no threshold)\n");
printf("arg7: Beginning index of mock galaxies\n\n");
exit(0); exit(0);
} }
adjfile = argv[1]; adjfile = argv[1];
@ -85,10 +82,6 @@ int main(int argc,char **argv) {
printf("Bad density threshold.\n"); printf("Bad density threshold.\n");
exit(0); exit(0);
} }
if (sscanf(argv[7],"%d",&mockIndex) == 0) {
printf("Bad mock galaxy index.\n");
exit(0);
}
printf("TOLERANCE: %f\n", voltol); printf("TOLERANCE: %f\n", voltol);
if (voltol <= 0.) { if (voltol <= 0.) {
printf("Proceeding without a density threshold.\n"); printf("Proceeding without a density threshold.\n");
@ -101,8 +94,6 @@ int main(int argc,char **argv) {
exit(0); exit(0);
} }
fread(&np,1, sizeof(int),adj); fread(&np,1, sizeof(int),adj);
if (mockIndex < 0)
mockIndex = np;
printf("adj: %d particles\n", np); printf("adj: %d particles\n", np);
FF; FF;
@ -158,7 +149,7 @@ int main(int argc,char **argv) {
for (i=0;i<np;i++) { for (i=0;i<np;i++) {
/* fread(&nin,1,sizeof(int),adj); /* actually nadj */ /* fread(&nin,1,sizeof(int),adj); /* actually nadj */
// PMS // PMS
if (p[i].ncnt != p[i].nadj && i < mockIndex) { if (p[i].ncnt != p[i].nadj && i < np) {
/*if (p[i].ncnt != p[i].nadj) {*/ /*if (p[i].ncnt != p[i].nadj) {*/
// END PMS // END PMS
p[i].nadj = p[i].ncnt; p[i].nadj = p[i].ncnt;
@ -183,10 +174,7 @@ int main(int argc,char **argv) {
FF; FF;
for (i=0;i<np;i++) { for (i=0;i<np;i++) {
fread(&p[i].dens,1,sizeof(float),vol); fread(&p[i].dens,1,sizeof(float),vol);
// PMS if ((p[i].dens < 1e-30) || (p[i].dens > 1e30)) {
if ((p[i].dens < 1e-30) || (p[i].dens > 1e30) && i < mockIndex) {
//if ((p[i].dens < 1e-30) || (p[i].dens > 1e30)) {
// END PMS
printf("Whacked-out volume found, of particle %d: %f\n",i,p[i].dens); printf("Whacked-out volume found, of particle %d: %f\n",i,p[i].dens);
p[i].dens = 1.; p[i].dens = 1.;
} }

21
c_source/zobov/vozinit.c
View file

@ -28,19 +28,17 @@ int main(int argc, char *argv[]) {
int numGuards; int numGuards;
int b[3]; int b[3];
int numThreads; int numThreads;
int mockIndex;
if (argc != 10) { if (argc != 9) {
printf("Wrong number of arguments.\n"); printf("Wrong number of arguments.\n");
printf("arg1: position file\n"); printf("arg1: position file\n");
printf("arg2: buffer size (default 0.1)\n"); printf("arg2: buffer size (default 0.1)\n");
printf("arg3: box size\n"); printf("arg3: box size\n");
printf("arg6: number of divisions (default 2)\n"); printf("arg4: number of divisions (default 2)\n");
printf("arg7: suffix describing this run\n"); printf("arg5: suffix describing this run\n");
printf("arg8: number of parallel threads\n"); printf("arg6: number of parallel threads\n");
printf("arg9: location of voboz executables\n"); printf("arg7: location of voboz executables\n");
printf("arg10: output directory\n"); printf("arg8: output directory\n");
printf("arg11: index of mock galaxies\n\n");
exit(0); exit(0);
} }
posfile = argv[1]; posfile = argv[1];
@ -72,11 +70,6 @@ int main(int argc, char *argv[]) {
} }
vobozPath = argv[7]; vobozPath = argv[7];
outDir = argv[8]; outDir = argv[8];
if (sscanf(argv[9],"%d",&mockIndex) != 1) {
printf("That's no mock galaxy index; try again.\n");
exit(0);
}
/* Read the position file */ /* Read the position file */
np = posread(posfile,&rfloat,1./boxsize); np = posread(posfile,&rfloat,1./boxsize);
@ -187,7 +180,7 @@ int main(int argc, char *argv[]) {
} }
} }
fprintf(scr,"wait\n"); fprintf(scr,"wait\n");
fprintf(scr,"%s/voztie %d %s %s %d\n", vobozPath, numdiv,suffix, outDir, mockIndex); fprintf(scr,"%s/voztie %d %s %s %d\n", vobozPath, numdiv,suffix, outDir);
fclose(scr); fclose(scr);
sprintf(systemstr,"chmod u+x %s",scrfile); sprintf(systemstr,"chmod u+x %s",scrfile);

46
c_source/zobov/voztie.c
View file

@ -34,10 +34,6 @@ int main(int argc, char *argv[]) {
int numRemoved = 0; int numRemoved = 0;
// PMS
int mockIndex;
// END PMS
if (argc != 5) { if (argc != 5) {
printf("Wrong number of arguments.\n"); printf("Wrong number of arguments.\n");
printf("arg1: number of divisions (default 2)\n"); printf("arg1: number of divisions (default 2)\n");
@ -57,10 +53,6 @@ int main(int argc, char *argv[]) {
suffix = argv[2]; suffix = argv[2];
outDir = argv[3]; outDir = argv[3];
if (sscanf(argv[4],"%d",&mockIndex) != 1) {
printf("That's no mock galaxy index; try again.\n");
exit(0);
}
np = -1; nvpmax = -1; nvpsum = 0; np = -1; nvpmax = -1; nvpsum = 0;
@ -92,10 +84,6 @@ int main(int argc, char *argv[]) {
printf("We have %d particles to tie together.\n",np); fflush(stdout); printf("We have %d particles to tie together.\n",np); fflush(stdout);
printf("The maximum number of particles in a file is %d.\n",nvpmax); printf("The maximum number of particles in a file is %d.\n",nvpmax);
// PMS
if (mockIndex == -1) mockIndex = np;
// END PMS
cnt_adj = (int *)malloc(np*sizeof(int)); cnt_adj = (int *)malloc(np*sizeof(int));
if (cnt_adj == NULL) if (cnt_adj == NULL)
printf("Could not allocate cnt_adj.\n"); printf("Could not allocate cnt_adj.\n");
@ -137,7 +125,7 @@ int main(int argc, char *argv[]) {
for (p=0;p<nvp;p++) { for (p=0;p<nvp;p++) {
fread(&volstemp,1,sizeof(float),part); fread(&volstemp,1,sizeof(float),part);
if (vols[orig[p]] > -1.) if (vols[orig[p]] > -1.)
if (fabs(vols[orig[p]]-volstemp)/volstemp > 1.5e-3 && orig[p] < mockIndex) { if (fabs(vols[orig[p]]-volstemp)/volstemp > 1.5e-3) {
printf("Inconsistent volumes for p. %d: (%10g,%10g)!\n", printf("Inconsistent volumes for p. %d: (%10g,%10g)!\n",
orig[p],vols[orig[p]],volstemp); orig[p],vols[orig[p]],volstemp);
//exit(0); //exit(0);
@ -183,16 +171,10 @@ int main(int argc, char *argv[]) {
// PMS : remove mock galaxies and anything adjacent to a mock galaxy // PMS : remove mock galaxies and anything adjacent to a mock galaxy
printf("\nRemoving mock galaxies...\n"); printf("\nRemoving mock galaxies...\n");
// completely unlink mock particles
for (i = mockIndex; i < np; i++) {
vols[i] = 1.e-29;
adjs[i].nadj = 0;
}
// unlink particles adjacent to mock galaxies // unlink particles adjacent to mock galaxies
for (i = 0; i < mockIndex; i++) { for (i = 0; i < np; i++) {
for (j = 0; j < adjs[i].nadj; j++) { for (j = 0; j < adjs[i].nadj; j++) {
if (adjs[i].adj[j] > mockIndex) { if (adjs[i].adj[j] > np) {
//printf("KILLING %d\n", i); //printf("KILLING %d\n", i);
vols[i] = 1.e-29; vols[i] = 1.e-29;
adjs[i].nadj = 0; adjs[i].nadj = 0;
@ -203,7 +185,7 @@ int main(int argc, char *argv[]) {
} }
// update all other adjacencies // update all other adjacencies
for (i = 0; i < mockIndex; i++) { for (i = 0; i < np; i++) {
int numAdjSaved = 0; int numAdjSaved = 0;
for (j = 0; j < adjs[i].nadj; j++) { for (j = 0; j < adjs[i].nadj; j++) {
@ -217,10 +199,6 @@ int main(int argc, char *argv[]) {
adjs[i].nadj = numAdjSaved; adjs[i].nadj = numAdjSaved;
} }
printf("Removed %d mock galaxies and %d adjacent galaxies.\n", np-mockIndex,
numRemoved);
printf("There are %d galaxies remaining.\n", mockIndex-numRemoved);
// END PMS // END PMS
*/ */
@ -254,19 +232,19 @@ int main(int argc, char *argv[]) {
printf("Unable to open %s\n",adjfile); printf("Unable to open %s\n",adjfile);
exit(0); exit(0);
} }
fwrite(&mockIndex,1, sizeof(int),adj); fwrite(&np,1, sizeof(int),adj);
/* Adjacencies: first the numbers of adjacencies, /* Adjacencies: first the numbers of adjacencies,
and the number we're actually going to write per particle */ and the number we're actually going to write per particle */
// Recount the number of adjacencies after merge // Recount the number of adjacencies after merge
for(i=0;i<mockIndex;i++) for(i=0;i<np;i++)
cnt_adj[i] = adjs[i].nadj; cnt_adj[i] = adjs[i].nadj;
for (i=0;i<mockIndex;i++) for (i=0;i<np;i++)
fwrite(&cnt_adj[i],1,sizeof(int),adj); fwrite(&cnt_adj[i],1,sizeof(int),adj);
/* Now the lists of adjacencies (without double counting) */ /* Now the lists of adjacencies (without double counting) */
for (i=0;i<mockIndex;i++) { for (i=0;i<np;i++) {
nout = 0; nout = 0;
for (j=0;j<adjs[i].nadj; j++) for (j=0;j<adjs[i].nadj; j++)
if (adjs[i].adj[j] > i) if (adjs[i].adj[j] > i)
@ -287,12 +265,8 @@ int main(int argc, char *argv[]) {
printf("Unable to open %s\n",volfile); printf("Unable to open %s\n",volfile);
exit(0); exit(0);
} }
// PMS fwrite(&np,1, sizeof(int),vol);
fwrite(&mockIndex,1, sizeof(int),vol); fwrite(vols,sizeof(float),np,vol);
fwrite(vols,sizeof(float),mockIndex,vol);
//fwrite(&np,1, sizeof(int),vol);
//fwrite(vols,sizeof(float),np,vol);
// END PMS
fclose(vol); fclose(vol);

61
python_source/backend/launchers.py
View file

@ -32,7 +32,6 @@ import shutil
import glob import glob
import subprocess import subprocess
import sys import sys
from pylab import figure
from netCDF4 import Dataset from netCDF4 import Dataset
from backend.classes import * from backend.classes import *
from backend.cosmologyTools import * from backend.cosmologyTools import *
@ -120,7 +119,7 @@ def launchPrep(sample, binPath, workDir=None, inputDataDir=None,
sample.zRange[1], sample.zRange[0], sample.zRange[1], "all", sample.zRange[1], sample.zRange[0], sample.zRange[1], "all",
sample.omegaM, useComoving=useComoving) sample.omegaM, useComoving=useComoving)
numTracers = int(open(outputDir+"/mask_index.txt", "r").read()) numTracers = int(open("total_particles.txt", "r").read())
sample.meanPartSep = (1.*numTracers/boxVol/nbar)**(-1/3.) sample.meanPartSep = (1.*numTracers/boxVol/nbar)**(-1/3.)
# flag edge galaxies with python routine for now # flag edge galaxies with python routine for now
@ -158,7 +157,7 @@ def launchPrep(sample, binPath, workDir=None, inputDataDir=None,
sample.zRange[1], sample.zRange[0], sample.zRange[1], "all", sample.zRange[1], sample.zRange[0], sample.zRange[1], "all",
sample.omegaM, useComoving=useComoving) sample.omegaM, useComoving=useComoving)
numTracers = int(open(outputDir+"/mask_index.txt", "r").read()) numTracers = int(open("total_particles.txt", "r").read())
sample.meanPartSep = (1.*numTracers/boxVol/nbar)**(-1/3.) sample.meanPartSep = (1.*numTracers/boxVol/nbar)**(-1/3.)
if os.access(parmFile, os.F_OK): os.unlink(parmFile) if os.access(parmFile, os.F_OK): os.unlink(parmFile)
@ -169,8 +168,7 @@ def launchPrep(sample, binPath, workDir=None, inputDataDir=None,
if os.access("comoving_distance.txt", os.F_OK): if os.access("comoving_distance.txt", os.F_OK):
os.system("mv %s %s" % ("comoving_distance.txt", outputDir)) os.system("mv %s %s" % ("comoving_distance.txt", outputDir))
if os.access("mask_index.txt", os.F_OK): if os.access("total_particles.txt", os.F_OK):
os.system("mv %s %s" % ("mask_index.txt", outputDir))
os.system("mv %s %s" % ("total_particles.txt", outputDir)) os.system("mv %s %s" % ("total_particles.txt", outputDir))
if os.access("galaxies.txt", os.F_OK): if os.access("galaxies.txt", os.F_OK):
@ -333,10 +331,8 @@ def launchPrep(sample, binPath, workDir=None, inputDataDir=None,
if os.access(parmFile, os.F_OK): if os.access(parmFile, os.F_OK):
os.unlink(parmFile) os.unlink(parmFile)
if os.access("mask_index.txt", os.F_OK): if os.access("total_particles.txt", os.F_OK):
os.system("mv %s %s" % ("mask_index.txt", outputDir))
os.system("mv %s %s" % ("total_particles.txt", outputDir)) os.system("mv %s %s" % ("total_particles.txt", outputDir))
#os.system("mv %s %s" % ("sample_info.txt", outputDir))
# save this sample's information # save this sample's information
with open(outputDir+"/sample_info.dat", mode='wb') as output: with open(outputDir+"/sample_info.dat", mode='wb') as output:
@ -382,15 +378,9 @@ def launchZobov(sample, binPath, outputDir=None, logDir=None, continueRun=None,
if os.access(vozScript, os.F_OK): if os.access(vozScript, os.F_OK):
os.unlink(vozScript) os.unlink(vozScript)
if sample.dataType == "observation": maxDen = mergingThreshold
maskIndex = open(outputDir+"/mask_index.txt", "r").read() if sample.dataType == "simulation" and numZobovDivisions == 1:
totalPart = open(outputDir+"/total_particles.txt", "r").read() print(" WARNING! You are using a single ZOBOV division with a simulation. Periodic boundaries will not be respected!")
maxDen = mergingThreshold*float(maskIndex)/float(totalPart)
else:
maskIndex = -1
maxDen = mergingThreshold
if numZobovDivisions == 1:
print(" WARNING! You are using a single ZOBOV division with a simulation. Periodic boundaries will not be respected!")
if not (continueRun and jobSuccessful(logFile, "Done!\n")): if not (continueRun and jobSuccessful(logFile, "Done!\n")):
for fileName in glob.glob(outputDir+"/part._"+sampleName+".*"): for fileName in glob.glob(outputDir+"/part._"+sampleName+".*"):
@ -404,7 +394,7 @@ def launchZobov(sample, binPath, outputDir=None, logDir=None, continueRun=None,
cmd = [binPath+"/vozinit", datafile, "0.1", "1.0", str(numZobovDivisions), \ cmd = [binPath+"/vozinit", datafile, "0.1", "1.0", str(numZobovDivisions), \
"_"+sampleName, str(numZobovThreads), \ "_"+sampleName, str(numZobovThreads), \
binPath, outputDir, str(maskIndex)] binPath, outputDir]
log = open(logFile, 'w') log = open(logFile, 'w')
subprocess.call(cmd, stdout=log, stderr=log) subprocess.call(cmd, stdout=log, stderr=log)
log.close() log.close()
@ -483,21 +473,24 @@ def launchZobov(sample, binPath, outputDir=None, logDir=None, continueRun=None,
else: else:
volFileToUse = outputDir+"/vol_"+sampleName+".dat" volFileToUse = outputDir+"/vol_"+sampleName+".dat"
# double-check to make sure galaxies were flagged correctly. # Zobov places guard particles at the domain walls; adjacenies to these
# if any non-edge galaxies have bad tesselations, flag them # guard particles are not tracked in the final tesselation.
# also, re-weight the volumes of any edge galaxies to prevent watershed # Therefore, if a galaxy marked as "interior" is missing an adjancency, that
# from spilling outside of survey region # means it erroneously connected to a guard particle.
#
# Re-weight the volumes of any edge galaxies to prevent watershed
# from spilling outside of survey region.
if sample.dataType == "observation": if sample.dataType == "observation":
log = open(logFile, 'a') log = open(logFile, 'a')
log.write("\nDouble-checking all edge flags.\n\n") log.write("\nDouble-checking all edge flags.\n")
# read in the edge flag information # read in the edge flag information
edgeFile = outputDir+"/galaxy_edge_flags.txt" edgeFile = outputDir+"/galaxy_edge_flags.txt"
edgeFlags = np.loadtxt(edgeFile, dtype=np.int32) edgeFlags = np.loadtxt(edgeFile, dtype=np.int32)
# load in and count adjacenies # load in and count adjacenies
log.write("Loading adjancies...\n") log.write(" Loading adjancies...\n")
part = [] part = []
adjFile = outputDir+"adj_"+sampleName+".dat" adjFile = outputDir+"adj_"+sampleName+".dat"
with open(adjFile, mode="rb") as File: with open(adjFile, mode="rb") as File:
@ -516,21 +509,18 @@ def launchZobov(sample, binPath, outputDir=None, logDir=None, continueRun=None,
part[p].adjs.append(pAdj) part[p].adjs.append(pAdj)
part[pAdj].adjs.append(p) part[pAdj].adjs.append(p)
# if the number of expected adjancies != actual adjacenies, this galaxy
# connected to a guard point on the boundary. This is fine for edge
# galaxies, but occasionally interior galaxies slip through the
# boundary handling, so we'll mark those as an edge
for p in range(numPart): for p in range(numPart):
nHave = len(part[p].adjs) nHave = len(part[p].adjs)
nExpected = nadjPerPart[p] nExpected = nadjPerPart[p]
#print("Working on %d: %d vs %d" % (p, nHave, nExpected))
if nHave != nExpected and edgeFlags[p] == 0: # an interior galaxy slipped through the boundary
log.write("Found an unflagged galaxy: %d. Correcting.\n" % (p)) if edgeFlags[p] == 0 and nHave != nExpected:
log.write(" Found an unflagged galaxy: %d. Correcting.\n" % (p))
edgeFlags[p] = 4 edgeFlags[p] = 4
# re-write the new edge flag information # re-write the new edge flag information
np.savetxt(edgeFile, edgeFlags, fmt="%d") np.savetxt(edgeFile, edgeFlags, fmt="%d")
log.write("\nDone double-checking. New flags saved.\n") log.write(" Done double-checking. New flags saved.\n")
# read in the appropriate volume file # read in the appropriate volume file
log.write("Re-weighting edge galaxy volumes...\n") log.write("Re-weighting edge galaxy volumes...\n")
@ -599,15 +589,11 @@ def launchPrune(sample, binPath,
open(outputDir+"/voidDesc_"+sampleName+".out")) open(outputDir+"/voidDesc_"+sampleName+".out"))
numVoids -= 2 numVoids -= 2
maxDen = mergingThreshold
if sample.dataType == "observation": if sample.dataType == "observation":
mockIndex = open(outputDir+"/mask_index.txt", "r").read()
totalPart = open(outputDir+"/total_particles.txt", "r").read() totalPart = open(outputDir+"/total_particles.txt", "r").read()
maxDen = mergingThreshold*float(mockIndex)/float(totalPart)
observationLine = " --isObservation" observationLine = " --isObservation"
#periodicLine = " --periodic=''"
else: else:
mockIndex = -1
maxDen = mergingThreshold
observationLine = "" observationLine = ""
periodicLine = " --periodic='" + getPeriodic(sample) + "'" periodicLine = " --periodic='" + getPeriodic(sample) + "'"
@ -646,7 +632,6 @@ def launchPrune(sample, binPath,
cmd += " --partEdge=" + outputDir+"galaxy_edge_flags.txt" cmd += " --partEdge=" + outputDir+"galaxy_edge_flags.txt"
cmd += " --extraInfo=" + outputDir+"/zobov_slice_"+str(sampleName)+".par" cmd += " --extraInfo=" + outputDir+"/zobov_slice_"+str(sampleName)+".par"
cmd += " --tolerance=" + str(boundaryTolerance) cmd += " --tolerance=" + str(boundaryTolerance)
cmd += " --mockIndex=" + str(mockIndex)
cmd += " --maxCentralDen=" + str(maxDen) cmd += " --maxCentralDen=" + str(maxDen)
cmd += " --zMin=" + str(sample.zRange[0]) cmd += " --zMin=" + str(sample.zRange[0])
cmd += " --zMax=" + str(sample.zRange[1]) cmd += " --zMax=" + str(sample.zRange[1])

25
python_source/voidUtil/catalogUtil.py
View file

@ -49,7 +49,6 @@ def loadPart(sampleDir):
ranges[2][0] = getattr(File, 'range_z_min') ranges[2][0] = getattr(File, 'range_z_min')
ranges[2][1] = getattr(File, 'range_z_max') ranges[2][1] = getattr(File, 'range_z_max')
isObservation = getattr(File, 'is_observation') isObservation = getattr(File, 'is_observation')
maskIndex = getattr(File, 'mask_index')
File.close() File.close()
mul = np.zeros((3)) mul = np.zeros((3))
mul[:] = ranges[:,1] - ranges[:,0] mul[:] = ranges[:,1] - ranges[:,0]
@ -100,24 +99,8 @@ def loadPart(sampleDir):
uniqueID = np.fromfile(File, dtype=np.int64,count=Np) uniqueID = np.fromfile(File, dtype=np.int64,count=Np)
chk = np.fromfile(File, dtype=np.int32,count=1) chk = np.fromfile(File, dtype=np.int32,count=1)
## TEST - outputting of mock particles is temporary for debugging
mockPart = []
if isObservation == 1:
mockPartx = x[maskIndex+1:Np]
mockParty = y[maskIndex+1:Np]
mockPartz = z[maskIndex+1:Np]
x = x[0:maskIndex]# * 100/300000
y = y[0:maskIndex]# * 100/300000
z = z[0:maskIndex]# * 100/300000
RA = RA[0:maskIndex]
Dec = Dec[0:maskIndex]
redshift = redshift[0:maskIndex]
uniqueID = uniqueID[0:maskIndex]
partData = np.column_stack((x,y,z)) partData = np.column_stack((x,y,z))
extraData = np.column_stack((RA,Dec,redshift,uniqueID)) extraData = np.column_stack((RA,Dec,redshift,uniqueID))
mockPart = np.column_stack((mockPartx, mockParty, mockPartz))
boxLen = mul boxLen = mul
@ -144,7 +127,7 @@ def loadPart(sampleDir):
isObservationData = isObservation == 1 isObservationData = isObservation == 1
return partData, boxLen, volNorm, isObservationData, ranges, extraData, mockPart return partData, boxLen, volNorm, isObservationData, ranges, extraData
# ----------------------------------------------------------------------------- # -----------------------------------------------------------------------------
def getVolNorm(sampleDir): def getVolNorm(sampleDir):
@ -161,7 +144,6 @@ def getVolNorm(sampleDir):
ranges[2][0] = getattr(File, 'range_z_min') ranges[2][0] = getattr(File, 'range_z_min')
ranges[2][1] = getattr(File, 'range_z_max') ranges[2][1] = getattr(File, 'range_z_max')
isObservation = getattr(File, 'is_observation') isObservation = getattr(File, 'is_observation')
maskIndex = getattr(File, 'mask_index')
File.close() File.close()
mul = np.zeros((3)) mul = np.zeros((3))
mul[:] = ranges[:,1] - ranges[:,0] mul[:] = ranges[:,1] - ranges[:,0]
@ -193,7 +175,7 @@ def getVolNorm(sampleDir):
selectionFuncFile=sample.selFunFile, selectionFuncFile=sample.selFunFile,
useComoving=sample.useComoving) useComoving=sample.useComoving)
boxVol = props[0] boxVol = props[0]
volNormObs = maskIndex/boxVol volNormObs = Np/boxVol
return volNorm, volNormObs return volNorm, volNormObs
@ -457,11 +439,10 @@ def loadVoidCatalog(sampleDir, dataPortion="central", loadParticles=True,
if loadParticles: if loadParticles:
print("Loading all particles...") print("Loading all particles...")
partData, boxLen, volNorm, isObservationData, ranges, extraData, mockPart = loadPart(sampleDir) partData, boxLen, volNorm, isObservationData, ranges, extraData = loadPart(sampleDir)
numPartTot = len(partData) numPartTot = len(partData)
catalog.numPartTot = numPartTot catalog.numPartTot = numPartTot
catalog.partPos = partData catalog.partPos = partData
catalog.mockPart = mockPart
catalog.part = [] catalog.part = []
for i in range(len(partData)): for i in range(len(partData)):
catalog.part.append(Bunch(x = partData[i][0], catalog.part.append(Bunch(x = partData[i][0],