mirror of
https://bitbucket.org/cosmicvoids/vide_public.git
synced 2025-07-04 15:21:11 +00:00
removed mock particle tracking, since that is no longer used
This commit is contained in:
Paul M. Sutter
parent
fc2d7157f4
commit
d9efa15474
8 changed files with 71 additions and 173 deletions
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@ -64,9 +64,6 @@ struct ParticleData
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vector<double> redshift;
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vector<double> catalogID;
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vector<long> uniqueID;
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// PMS
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int mask_index;
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// END PMS
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int edgeFlag = 0;
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vector<Position> pos;
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double box[3][2];
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@ -263,12 +260,8 @@ void flagEdgeGalaxies(prepObservation_info& args ,
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size_t nEval;
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//End Maubert - Needed for comobile distance in mock_sphere
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// TODO - REMOVE THIS
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output_data.mask_index = output_data.id_gal.size();
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// write a small text file with galaxy position (for diagnostic purposes)
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// TODO - remove this
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FILE *fp;
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fp = fopen("galaxies.txt", "w");
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//for (int i = 0; i < output_data.id_gal.size(); i++) {
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@ -414,11 +407,9 @@ void saveForZobov(ParticleData& pdata, const string& fname,
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fp.putAtt("range_y_max", ncDouble, Lmax/100.);
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fp.putAtt("range_z_min", ncDouble, -Lmax/100.);
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fp.putAtt("range_z_max", ncDouble, Lmax/100.);
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fp.putAtt("mask_index", ncInt, pdata.mask_index); // PMS
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fp.putAtt("is_observation", ncInt, 1); // PMS
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fp.putAtt("is_observation", ncInt, 1);
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int nOutputPart = pdata.mask_index;
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//int nOutputPart = pdata.pos.size();
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int nOutputPart = pdata.pos.size();
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NcDim NumPart_dim = fp.addDim("numpart_dim", nOutputPart);
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NcVar v = fp.addVar("particle_ids", ncInt, NumPart_dim);
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@ -497,10 +488,7 @@ int main(int argc, char **argv)
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saveForZobov(output_data, args_info.output_arg, args_info.params_arg);
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// PMS - TODO REMOVE THIS
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FILE *fp = fopen("mask_index.txt", "w");
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fprintf(fp, "%d", output_data.mask_index);
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fclose(fp);
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FILE *fp;
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fp = fopen("total_particles.txt", "w");
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fprintf(fp, "%d", output_data.pos.size());
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fclose(fp);
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@ -116,7 +116,7 @@ double expanFun (double z, void * p) {
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void openFiles(string outputDir, string sampleName,
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string prefix, string dataPortion,
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int mockIndex, int numKept,
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int numPartTot, int numKept,
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FILE** fpZobov, FILE** fpCenters,
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FILE** fpCentersNoCut,
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FILE** fpBarycenter, FILE** fpShapes,
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@ -128,7 +128,7 @@ void closeFiles(FILE* fpZobov, FILE* fpCenters,
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FILE* fpSkyPositions);
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void outputVoids(string outputDir, string sampleName, string prefix,
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string dataPortion, int mockIndex,
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string dataPortion, int numPartTot,
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vector<VOID> voids,
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bool isObservation, double *boxLen,
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bool doTrim, bool doCentralDenCut);
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@ -187,7 +187,7 @@ int main(int argc, char **argv) {
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int i, p, p2, numPartTot, numZonesTot, dummy, iVoid;
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int numVoids, mockIndex;
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int numVoids;
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double tolerance;
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FILE *fp;
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PART *part, *voidPart, *flaggedPart;
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@ -202,7 +202,6 @@ int main(int argc, char **argv) {
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double nearestEdge, redshift;
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char line[500], junkStr[10];
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string outputDir, sampleName, dataPortion, prefix;
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int mask_index;
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double ranges[3][2], boxLen[3], mul;
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double volNorm, radius;
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int clock1, clock2, clock3, clock4;
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@ -213,7 +212,6 @@ int main(int argc, char **argv) {
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gsl_eigen_symmv_workspace *eigw = gsl_eigen_symmv_alloc(3);
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numVoids = args.numVoids_arg;
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mockIndex = args.mockIndex_arg;
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tolerance = args.tolerance_arg;
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clock1 = clock();
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@ -309,9 +307,6 @@ int main(int argc, char **argv) {
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interval = 1.*(clock4 - clock3)/CLOCKS_PER_SEC;
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printf(" Read %d particles (%.2f sec)...\n", numPartTot, interval);
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if (mockIndex == -1) mockIndex = numPartTot;
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// read in desired voids
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clock3 = clock();
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printf(" Loading voids...\n");
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@ -393,12 +388,8 @@ int main(int argc, char **argv) {
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// and volumes
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printf(" Loading particle volumes...\n");
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fp = fopen(args.partVol_arg, "r");
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fread(&mask_index, 1, 4, fp);
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if (mask_index != mockIndex) {
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printf("NON-MATCHING MOCK INDICES!? %d %d\n", mask_index, mockIndex);
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exit(-1);
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}
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for (p = 0; p < mask_index; p++) {
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fread(&numPartTot, 1, 4, fp);
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for (p = 0; p < numPartTot; p++) {
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fread(&temp[0], 1, 4, fp);
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part[p].vol = temp[0];
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}
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@ -408,7 +399,7 @@ int main(int argc, char **argv) {
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printf(" Loading particle edge flags...\n");
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int numFlagged = 0;
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fp = fopen(args.partEdge_arg, "r");
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for (p = 0; p < mask_index; p++) {
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for (p = 0; p < numPartTot; p++) {
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fscanf(fp, "%d", &part[p].edgeFlag);
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if (part[p].edgeFlag > 0) numFlagged++;
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}
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@ -417,7 +408,7 @@ int main(int argc, char **argv) {
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// copy flagged galaxies to separate array for faster processing later
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flaggedPart = (PART *) malloc(numFlagged * sizeof(PART));
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int iFlag = 0;
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for (p = 0; p < mask_index; p++) {
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for (p = 0; p < numPartTot; p++) {
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if (part[p].edgeFlag > 0) {
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flaggedPart[iFlag] = part[p];
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iFlag++;
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@ -428,20 +419,20 @@ int main(int argc, char **argv) {
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// and finally finally adjacencies
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printf(" Loading particle adjacencies...\n");
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fp = fopen(args.partAdj_arg, "r");
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fread(&mask_index, 1, 4, fp);
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if (mask_index != mockIndex) {
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printf("NON-MATCHING MOCK INDICES!? %d %d\n", mask_index, mockIndex);
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fread(&numPartTot, 1, 4, fp);
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if (numPartTot != numPartTot) {
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printf("NON-MATCHING MOCK INDICES!? %d %d\n", numPartTot, numPartTot);
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exit(-1);
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}
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int tempInt;
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for (p = 0; p < mask_index; p++) {
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for (p = 0; p < numPartTot; p++) {
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fread(&tempInt, 1, 4, fp);
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part[p].nadj = tempInt;
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part[p].ncnt = 0;
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if (part[p].nadj > 0)
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part[p].adj = (int *) malloc(part[p].nadj * sizeof(int));
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}
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for (p = 0; p < mask_index; p++) {
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for (p = 0; p < numPartTot; p++) {
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fread(&tempInt, 1, 4, fp);
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int nin = tempInt;
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if (nin > 0) {
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@ -452,7 +443,7 @@ int main(int argc, char **argv) {
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// this bit has been readjusted just in case we are
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// accidentally still linking to mock particles
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//if (tempAdj < mask_index) {
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//if (tempAdj < numPartTot) {
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assert(p < tempAdj);
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//if (part[p].ncnt == part[p].nadj) {
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// printf("OVERFLOW %d\n", p);
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@ -461,7 +452,7 @@ int main(int argc, char **argv) {
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//} else {
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part[p].adj[part[p].ncnt] = tempAdj;
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part[p].ncnt++;
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if (tempAdj < mask_index) {
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if (tempAdj < numPartTot) {
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part[tempAdj].adj[part[tempAdj].ncnt] = p;
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part[tempAdj].ncnt++;
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}
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@ -542,9 +533,8 @@ int main(int argc, char **argv) {
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partID = zones2Parts[zoneID].partIDs[p];
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// something went haywire
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if (partID > mask_index ||
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(part[partID].vol < 1.e-27 && part[partID].vol > 0.)) {
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printf("BAD PART!? %d %d %e", partID, mask_index, part[partID].vol);
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if (part[partID].vol < 1.e-27 && part[partID].vol > 0.) {
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printf("BAD PART!? %d %d %e", partID, numPartTot, part[partID].vol);
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exit(-1);
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}
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@ -567,7 +557,7 @@ int main(int argc, char **argv) {
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//printf("NORMAL!! %d %d %e\n", iVoid, partID, part[partID].vol);
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}
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for (int iAdj = 0; iAdj < part[partID].ncnt; iAdj++) {
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if (part[partID].adj[iAdj] > mockIndex) {
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if (part[partID].adj[iAdj] > numPartTot) {
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printf("CONTAMINATED!! %d %d %d\n", iVoid, partID, iAdj);
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}
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}
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@ -949,7 +939,7 @@ int main(int argc, char **argv) {
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for (int i = 0; i < 2; i++) {
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dataPortion = dataPortions[i];
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outputVoids(outputDir, sampleName, prefix, dataPortion,
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mockIndex,
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numPartTot,
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voids,
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args.isObservation_flag, boxLen, true, true);
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}
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@ -959,7 +949,7 @@ int main(int argc, char **argv) {
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for (int i = 0; i < 2; i++) {
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dataPortion = dataPortions[i];
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outputVoids(outputDir, sampleName, prefix, dataPortion,
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mockIndex,
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numPartTot,
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voids,
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args.isObservation_flag, boxLen, false, false);
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}
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@ -977,14 +967,14 @@ int main(int argc, char **argv) {
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// ----------------------------------------------------------------------------
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void openFiles(string outputDir, string sampleName,
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string prefix, string dataPortion,
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int mockIndex, int numKept,
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int numPartTot, int numKept,
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FILE** fpZobov, FILE** fpCenters,
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FILE** fpBarycenter, FILE** fpShapes,
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FILE** fpExtra,
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FILE** fpSkyPositions) {
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*fpZobov = fopen((outputDir+"/"+prefix+"voidDesc_"+dataPortion+"_"+sampleName).c_str(), "w");
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fprintf(*fpZobov, "%d particles, %d voids.\n", mockIndex, numKept);
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fprintf(*fpZobov, "%d particles, %d voids.\n", numPartTot, numKept);
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fprintf(*fpZobov, "Void# FileVoid# CoreParticle CoreDens ZoneVol Zone#Part Void#Zones VoidVol Void#Part VoidDensContrast VoidProb\n");
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*fpBarycenter = fopen((outputDir+"/"+prefix+"macrocenters_"+dataPortion+"_"+sampleName).c_str(), "w");
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@ -1022,7 +1012,7 @@ void closeFiles(FILE* fpZobov, FILE* fpCenters,
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// ----------------------------------------------------------------------------
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void outputVoids(string outputDir, string sampleName, string prefix,
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string dataPortion, int mockIndex,
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string dataPortion, int numPartTot,
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vector<VOID> voids,
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bool isObservation, double *boxLen, bool doTrim,
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bool doCentralDenCut) {
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@ -1034,7 +1024,7 @@ void outputVoids(string outputDir, string sampleName, string prefix,
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openFiles(outputDir, sampleName, prefix, dataPortion,
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mockIndex, voids.size(),
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numPartTot, voids.size(),
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&fpZobov, &fpCenters, &fpBarycenter,
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&fpShapes, &fpExtra, &fpSkyPositions);
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@ -19,7 +19,6 @@ option "partAdj" - "Adjacency file from ZOBOV" string required
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option "partEdge" - "Boundary flag file" string required
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option "zone2Part" - "Particle file from ZOBOV" string required
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option "mockIndex" - "Beginning index of mock particles" int required
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option "numVoids" - "Number of voids" int required
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@ -61,8 +61,6 @@ int main(int argc,char **argv) {
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double *sorter, e1,maxdenscontrast;
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int *iord;
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int mockIndex;
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e1 = exp(1.)-1.;
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if (argc != 8) {
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@ -73,7 +71,6 @@ int main(int argc,char **argv) {
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printf("arg4: output file containing zones in each void\n");
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printf("arg5: output text file\n");
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printf("arg6: Density threshold (0 for no threshold)\n");
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printf("arg7: Beginning index of mock galaxies\n\n");
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exit(0);
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}
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adjfile = argv[1];
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@ -85,10 +82,6 @@ int main(int argc,char **argv) {
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printf("Bad density threshold.\n");
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exit(0);
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}
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if (sscanf(argv[7],"%d",&mockIndex) == 0) {
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printf("Bad mock galaxy index.\n");
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exit(0);
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}
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printf("TOLERANCE: %f\n", voltol);
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if (voltol <= 0.) {
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printf("Proceeding without a density threshold.\n");
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@ -101,8 +94,6 @@ int main(int argc,char **argv) {
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exit(0);
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}
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fread(&np,1, sizeof(int),adj);
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if (mockIndex < 0)
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mockIndex = np;
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printf("adj: %d particles\n", np);
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FF;
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@ -158,7 +149,7 @@ int main(int argc,char **argv) {
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for (i=0;i<np;i++) {
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/* fread(&nin,1,sizeof(int),adj); /* actually nadj */
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// PMS
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if (p[i].ncnt != p[i].nadj && i < mockIndex) {
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if (p[i].ncnt != p[i].nadj && i < np) {
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/*if (p[i].ncnt != p[i].nadj) {*/
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// END PMS
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p[i].nadj = p[i].ncnt;
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@ -183,10 +174,7 @@ int main(int argc,char **argv) {
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FF;
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for (i=0;i<np;i++) {
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fread(&p[i].dens,1,sizeof(float),vol);
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// PMS
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if ((p[i].dens < 1e-30) || (p[i].dens > 1e30) && i < mockIndex) {
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//if ((p[i].dens < 1e-30) || (p[i].dens > 1e30)) {
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// END PMS
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if ((p[i].dens < 1e-30) || (p[i].dens > 1e30)) {
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printf("Whacked-out volume found, of particle %d: %f\n",i,p[i].dens);
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p[i].dens = 1.;
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}
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@ -28,19 +28,17 @@ int main(int argc, char *argv[]) {
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int numGuards;
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int b[3];
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int numThreads;
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int mockIndex;
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if (argc != 10) {
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if (argc != 9) {
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printf("Wrong number of arguments.\n");
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printf("arg1: position file\n");
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printf("arg2: buffer size (default 0.1)\n");
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printf("arg3: box size\n");
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printf("arg6: number of divisions (default 2)\n");
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printf("arg7: suffix describing this run\n");
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printf("arg8: number of parallel threads\n");
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printf("arg9: location of voboz executables\n");
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printf("arg10: output directory\n");
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printf("arg11: index of mock galaxies\n\n");
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printf("arg4: number of divisions (default 2)\n");
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printf("arg5: suffix describing this run\n");
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printf("arg6: number of parallel threads\n");
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printf("arg7: location of voboz executables\n");
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printf("arg8: output directory\n");
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exit(0);
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}
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posfile = argv[1];
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@ -72,11 +70,6 @@ int main(int argc, char *argv[]) {
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}
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vobozPath = argv[7];
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outDir = argv[8];
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if (sscanf(argv[9],"%d",&mockIndex) != 1) {
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printf("That's no mock galaxy index; try again.\n");
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exit(0);
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}
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/* Read the position file */
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np = posread(posfile,&rfloat,1./boxsize);
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@ -187,7 +180,7 @@ int main(int argc, char *argv[]) {
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}
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}
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fprintf(scr,"wait\n");
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fprintf(scr,"%s/voztie %d %s %s %d\n", vobozPath, numdiv,suffix, outDir, mockIndex);
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fprintf(scr,"%s/voztie %d %s %s %d\n", vobozPath, numdiv,suffix, outDir);
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fclose(scr);
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sprintf(systemstr,"chmod u+x %s",scrfile);
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@ -34,10 +34,6 @@ int main(int argc, char *argv[]) {
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int numRemoved = 0;
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// PMS
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int mockIndex;
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// END PMS
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if (argc != 5) {
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printf("Wrong number of arguments.\n");
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printf("arg1: number of divisions (default 2)\n");
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@ -57,10 +53,6 @@ int main(int argc, char *argv[]) {
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suffix = argv[2];
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outDir = argv[3];
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if (sscanf(argv[4],"%d",&mockIndex) != 1) {
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printf("That's no mock galaxy index; try again.\n");
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exit(0);
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}
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np = -1; nvpmax = -1; nvpsum = 0;
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@ -92,10 +84,6 @@ int main(int argc, char *argv[]) {
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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);
|
||||
|
||||
// PMS
|
||||
if (mockIndex == -1) mockIndex = np;
|
||||
// END PMS
|
||||
|
||||
cnt_adj = (int *)malloc(np*sizeof(int));
|
||||
if (cnt_adj == NULL)
|
||||
printf("Could not allocate cnt_adj.\n");
|
||||
|
|
@ -137,7 +125,7 @@ int main(int argc, char *argv[]) {
|
|||
for (p=0;p<nvp;p++) {
|
||||
fread(&volstemp,1,sizeof(float),part);
|
||||
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",
|
||||
orig[p],vols[orig[p]],volstemp);
|
||||
//exit(0);
|
||||
|
|
@ -183,16 +171,10 @@ int main(int argc, char *argv[]) {
|
|||
// PMS : remove mock galaxies and anything adjacent to a mock galaxy
|
||||
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
|
||||
for (i = 0; i < mockIndex; i++) {
|
||||
for (i = 0; i < np; i++) {
|
||||
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);
|
||||
vols[i] = 1.e-29;
|
||||
adjs[i].nadj = 0;
|
||||
|
|
@ -203,7 +185,7 @@ int main(int argc, char *argv[]) {
|
|||
}
|
||||
|
||||
// update all other adjacencies
|
||||
for (i = 0; i < mockIndex; i++) {
|
||||
for (i = 0; i < np; i++) {
|
||||
|
||||
int numAdjSaved = 0;
|
||||
for (j = 0; j < adjs[i].nadj; j++) {
|
||||
|
|
@ -217,10 +199,6 @@ int main(int argc, char *argv[]) {
|
|||
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
|
||||
*/
|
||||
|
||||
|
|
@ -254,19 +232,19 @@ int main(int argc, char *argv[]) {
|
|||
printf("Unable to open %s\n",adjfile);
|
||||
exit(0);
|
||||
}
|
||||
fwrite(&mockIndex,1, sizeof(int),adj);
|
||||
fwrite(&np,1, sizeof(int),adj);
|
||||
/* Adjacencies: first the numbers of adjacencies,
|
||||
and the number we're actually going to write per particle */
|
||||
|
||||
// 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;
|
||||
|
||||
for (i=0;i<mockIndex;i++)
|
||||
for (i=0;i<np;i++)
|
||||
fwrite(&cnt_adj[i],1,sizeof(int),adj);
|
||||
|
||||
/* Now the lists of adjacencies (without double counting) */
|
||||
for (i=0;i<mockIndex;i++) {
|
||||
for (i=0;i<np;i++) {
|
||||
nout = 0;
|
||||
for (j=0;j<adjs[i].nadj; j++)
|
||||
if (adjs[i].adj[j] > i)
|
||||
|
|
@ -287,12 +265,8 @@ int main(int argc, char *argv[]) {
|
|||
printf("Unable to open %s\n",volfile);
|
||||
exit(0);
|
||||
}
|
||||
// PMS
|
||||
fwrite(&mockIndex,1, sizeof(int),vol);
|
||||
fwrite(vols,sizeof(float),mockIndex,vol);
|
||||
//fwrite(&np,1, sizeof(int),vol);
|
||||
//fwrite(vols,sizeof(float),np,vol);
|
||||
// END PMS
|
||||
fwrite(&np,1, sizeof(int),vol);
|
||||
fwrite(vols,sizeof(float),np,vol);
|
||||
|
||||
fclose(vol);
|
||||
|
||||
|
|
|
|||
|
|
@ -32,7 +32,6 @@ import shutil
|
|||
import glob
|
||||
import subprocess
|
||||
import sys
|
||||
from pylab import figure
|
||||
from netCDF4 import Dataset
|
||||
from backend.classes 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.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.)
|
||||
|
||||
# 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.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.)
|
||||
|
||||
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):
|
||||
os.system("mv %s %s" % ("comoving_distance.txt", outputDir))
|
||||
|
||||
if os.access("mask_index.txt", os.F_OK):
|
||||
os.system("mv %s %s" % ("mask_index.txt", outputDir))
|
||||
if os.access("total_particles.txt", os.F_OK):
|
||||
os.system("mv %s %s" % ("total_particles.txt", outputDir))
|
||||
|
||||
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):
|
||||
os.unlink(parmFile)
|
||||
|
||||
if os.access("mask_index.txt", os.F_OK):
|
||||
os.system("mv %s %s" % ("mask_index.txt", outputDir))
|
||||
if os.access("total_particles.txt", os.F_OK):
|
||||
os.system("mv %s %s" % ("total_particles.txt", outputDir))
|
||||
#os.system("mv %s %s" % ("sample_info.txt", outputDir))
|
||||
|
||||
# save this sample's information
|
||||
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):
|
||||
os.unlink(vozScript)
|
||||
|
||||
if sample.dataType == "observation":
|
||||
maskIndex = open(outputDir+"/mask_index.txt", "r").read()
|
||||
totalPart = open(outputDir+"/total_particles.txt", "r").read()
|
||||
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!")
|
||||
maxDen = mergingThreshold
|
||||
if sample.dataType == "simulation" and 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")):
|
||||
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), \
|
||||
"_"+sampleName, str(numZobovThreads), \
|
||||
binPath, outputDir, str(maskIndex)]
|
||||
binPath, outputDir]
|
||||
log = open(logFile, 'w')
|
||||
subprocess.call(cmd, stdout=log, stderr=log)
|
||||
log.close()
|
||||
|
|
@ -483,21 +473,24 @@ def launchZobov(sample, binPath, outputDir=None, logDir=None, continueRun=None,
|
|||
else:
|
||||
volFileToUse = outputDir+"/vol_"+sampleName+".dat"
|
||||
|
||||
# double-check to make sure galaxies were flagged correctly.
|
||||
# if any non-edge galaxies have bad tesselations, flag them
|
||||
# also, re-weight the volumes of any edge galaxies to prevent watershed
|
||||
# from spilling outside of survey region
|
||||
# Zobov places guard particles at the domain walls; adjacenies to these
|
||||
# guard particles are not tracked in the final tesselation.
|
||||
# Therefore, if a galaxy marked as "interior" is missing an adjancency, that
|
||||
# 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":
|
||||
|
||||
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
|
||||
edgeFile = outputDir+"/galaxy_edge_flags.txt"
|
||||
edgeFlags = np.loadtxt(edgeFile, dtype=np.int32)
|
||||
|
||||
# load in and count adjacenies
|
||||
log.write("Loading adjancies...\n")
|
||||
log.write(" Loading adjancies...\n")
|
||||
part = []
|
||||
adjFile = outputDir+"adj_"+sampleName+".dat"
|
||||
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[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):
|
||||
nHave = len(part[p].adjs)
|
||||
nExpected = nadjPerPart[p]
|
||||
#print("Working on %d: %d vs %d" % (p, nHave, nExpected))
|
||||
if nHave != nExpected and edgeFlags[p] == 0:
|
||||
log.write("Found an unflagged galaxy: %d. Correcting.\n" % (p))
|
||||
|
||||
# an interior galaxy slipped through the boundary
|
||||
if edgeFlags[p] == 0 and nHave != nExpected:
|
||||
log.write(" Found an unflagged galaxy: %d. Correcting.\n" % (p))
|
||||
edgeFlags[p] = 4
|
||||
|
||||
# re-write the new edge flag information
|
||||
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
|
||||
log.write("Re-weighting edge galaxy volumes...\n")
|
||||
|
|
@ -599,15 +589,11 @@ def launchPrune(sample, binPath,
|
|||
open(outputDir+"/voidDesc_"+sampleName+".out"))
|
||||
numVoids -= 2
|
||||
|
||||
maxDen = mergingThreshold
|
||||
if sample.dataType == "observation":
|
||||
mockIndex = open(outputDir+"/mask_index.txt", "r").read()
|
||||
totalPart = open(outputDir+"/total_particles.txt", "r").read()
|
||||
maxDen = mergingThreshold*float(mockIndex)/float(totalPart)
|
||||
observationLine = " --isObservation"
|
||||
#periodicLine = " --periodic=''"
|
||||
else:
|
||||
mockIndex = -1
|
||||
maxDen = mergingThreshold
|
||||
observationLine = ""
|
||||
|
||||
periodicLine = " --periodic='" + getPeriodic(sample) + "'"
|
||||
|
|
@ -646,7 +632,6 @@ def launchPrune(sample, binPath,
|
|||
cmd += " --partEdge=" + outputDir+"galaxy_edge_flags.txt"
|
||||
cmd += " --extraInfo=" + outputDir+"/zobov_slice_"+str(sampleName)+".par"
|
||||
cmd += " --tolerance=" + str(boundaryTolerance)
|
||||
cmd += " --mockIndex=" + str(mockIndex)
|
||||
cmd += " --maxCentralDen=" + str(maxDen)
|
||||
cmd += " --zMin=" + str(sample.zRange[0])
|
||||
cmd += " --zMax=" + str(sample.zRange[1])
|
||||
|
|
|
|||
|
|
@ -49,7 +49,6 @@ def loadPart(sampleDir):
|
|||
ranges[2][0] = getattr(File, 'range_z_min')
|
||||
ranges[2][1] = getattr(File, 'range_z_max')
|
||||
isObservation = getattr(File, 'is_observation')
|
||||
maskIndex = getattr(File, 'mask_index')
|
||||
File.close()
|
||||
mul = np.zeros((3))
|
||||
mul[:] = ranges[:,1] - ranges[:,0]
|
||||
|
|
@ -100,24 +99,8 @@ def loadPart(sampleDir):
|
|||
uniqueID = np.fromfile(File, dtype=np.int64,count=Np)
|
||||
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))
|
||||
extraData = np.column_stack((RA,Dec,redshift,uniqueID))
|
||||
mockPart = np.column_stack((mockPartx, mockParty, mockPartz))
|
||||
|
||||
boxLen = mul
|
||||
|
||||
|
|
@ -144,7 +127,7 @@ def loadPart(sampleDir):
|
|||
|
||||
isObservationData = isObservation == 1
|
||||
|
||||
return partData, boxLen, volNorm, isObservationData, ranges, extraData, mockPart
|
||||
return partData, boxLen, volNorm, isObservationData, ranges, extraData
|
||||
|
||||
# -----------------------------------------------------------------------------
|
||||
def getVolNorm(sampleDir):
|
||||
|
|
@ -161,7 +144,6 @@ def getVolNorm(sampleDir):
|
|||
ranges[2][0] = getattr(File, 'range_z_min')
|
||||
ranges[2][1] = getattr(File, 'range_z_max')
|
||||
isObservation = getattr(File, 'is_observation')
|
||||
maskIndex = getattr(File, 'mask_index')
|
||||
File.close()
|
||||
mul = np.zeros((3))
|
||||
mul[:] = ranges[:,1] - ranges[:,0]
|
||||
|
|
@ -193,7 +175,7 @@ def getVolNorm(sampleDir):
|
|||
selectionFuncFile=sample.selFunFile,
|
||||
useComoving=sample.useComoving)
|
||||
boxVol = props[0]
|
||||
volNormObs = maskIndex/boxVol
|
||||
volNormObs = Np/boxVol
|
||||
|
||||
return volNorm, volNormObs
|
||||
|
||||
|
|
@ -457,11 +439,10 @@ def loadVoidCatalog(sampleDir, dataPortion="central", loadParticles=True,
|
|||
|
||||
if loadParticles:
|
||||
print("Loading all particles...")
|
||||
partData, boxLen, volNorm, isObservationData, ranges, extraData, mockPart = loadPart(sampleDir)
|
||||
partData, boxLen, volNorm, isObservationData, ranges, extraData = loadPart(sampleDir)
|
||||
numPartTot = len(partData)
|
||||
catalog.numPartTot = numPartTot
|
||||
catalog.partPos = partData
|
||||
catalog.mockPart = mockPart
|
||||
catalog.part = []
|
||||
for i in range(len(partData)):
|
||||
catalog.part.append(Bunch(x = partData[i][0],
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue