mirror of
https://bitbucket.org/cosmicvoids/vide_public.git
synced 2025-07-04 23:31:12 +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);
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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);
|
||||
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue