From 3c8d7b2fb29d86a9421f074454a2714b7691606c Mon Sep 17 00:00:00 2001 From: "P.M. Sutter" Date: Thu, 20 Dec 2012 13:38:14 -0600 Subject: [PATCH 1/7] significant speedups to void matching algorithm --- c_tools/analysis/voidOverlap.cpp | 122 ++++++++++++++----------------- 1 file changed, 55 insertions(+), 67 deletions(-) diff --git a/c_tools/analysis/voidOverlap.cpp b/c_tools/analysis/voidOverlap.cpp index 0d1df14..37f9a9f 100644 --- a/c_tools/analysis/voidOverlap.cpp +++ b/c_tools/analysis/voidOverlap.cpp @@ -88,6 +88,8 @@ int main(int argc, char **argv) { int closestMatchID; float closestMatchDist; float commonVolRatio; + MATCHPROPS newMatch; + int MAX_MATCHES = 20; CATALOG catalog1, catalog2; @@ -134,38 +136,44 @@ int main(int argc, char **argv) { printf("Will assume z-direction is periodic.\n"); } - printf(" Determining overlap...\n"); - -/* - // just use centers + // find closest voids + printf(" Finding nearest matches...\n"); for (iVoid1 = 0; iVoid1 < catalog1.numVoids; iVoid1++) { - closestMatchDist = 1.e99; for (iVoid2 = 0; iVoid2 < catalog2.numVoids; iVoid2++) { rdist = getDist(catalog1, catalog2, iVoid1, iVoid2, periodicX, periodicY, periodicZ); - if (rdist < closestMatchDist) { - closestMatchID = iVoid2; - closestMatchDist = rdist; + + newMatch.matchID = iVoid2; + newMatch.commonVol = 0; + newMatch.dist = rdist; + + if (catalog1.voids[iVoid1].matches.size() < MAX_MATCHES) { + catalog1.voids[iVoid1].matches.push_back(newMatch); + } else { + // find the farthest match + float farthestMatchDist = 0; + int farthestMatchID = 0; + for (iMatch = 0; iMatch < MAX_MATCHES; iMatch++) { + if (catalog1.voids[iVoid1].matches[iMatch].dist > farthestMatchDist){ + farthestMatchDist = catalog1.voids[iVoid1].matches[iMatch].dist; + farthestMatchID = iMatch; + } + } + if (rdist < farthestMatchDist) + catalog1.voids[iVoid1].matches[farthestMatchID] = newMatch; } - - } - - MATCHPROPS newMatch; - newMatch.matchID = closestMatchID; - newMatch.commonVol = 1; - newMatch.dist = closestMatchDist; - catalog1.voids[iVoid1].matches.push_back(newMatch); + } } -*/ + printf(" Determining overlap...\n"); for (iVoid1 = 0; iVoid1 < catalog1.numVoids; iVoid1++) { - printf(" Working on void %d of %d...\n", iVoid1, catalog1.numVoids); + printf(" Working on void %d of %d...\n", iVoid1+1, catalog1.numVoids); voidID1 = catalog1.voids[iVoid1].voidID; - for (iVoid2 = 0; iVoid2 < catalog2.numVoids; iVoid2++) { + for (iMatch = 0; iMatch < catalog1.voids[iVoid1].matches.size();iMatch++) { + iVoid2 = catalog1.voids[iVoid1].matches[iMatch].matchID; voidID2 = catalog2.voids[iVoid2].voidID; - match = false; for (iZ1 = 0; iZ1 < catalog1.void2Zones[voidID1].numZones; iZ1++) { zoneID1 = catalog1.void2Zones[voidID1].zoneIDs[iZ1]; @@ -180,6 +188,7 @@ int main(int argc, char **argv) { partID2 = catalog2.zones2Parts[zoneID2].partIDs[p2]; match = false; + if (args.useID_flag) { if (catalog1.part[partID1].uniqueID == catalog2.part[partID2].uniqueID) match = true; @@ -203,35 +212,12 @@ int main(int argc, char **argv) { r2 = pow(3./4./M_PI*catalog2.part[partID2].volume / catalog2.numPartTot, 1./3.); if (rdist <= 0.1*r1 || rdist <= 0.1*r2) match = true; - } + } - if (match) { - bool alreadyMatched = false; - for (iMatch = 0; - iMatch < catalog1.voids[iVoid1].matches.size(); iMatch++) { - if (catalog1.voids[iVoid1].matches[iMatch].matchID == - iVoid2) { - alreadyMatched = true; - break; - } - } - - if (alreadyMatched) { - //catalog1.voids[iVoid1].matches[iMatch].commonVol += 1; - catalog1.voids[iVoid1].matches[iMatch].commonVol += - catalog1.part[partID1].volume; - } else { - MATCHPROPS newMatch; - newMatch.matchID = iVoid2; - //newMatch.commonVol = 1; - newMatch.commonVol = catalog1.part[partID1].volume; - - newMatch.dist = getDist(catalog1, catalog2, iVoid1, iVoid2, - periodicX, periodicY, periodicZ); - catalog1.voids[iVoid1].matches.push_back(newMatch); - } // end if match - } + catalog1.voids[iVoid1].matches[iMatch].commonVol += + catalog2.part[partID2].volume; + } // end if match } // end p2 } // end iZ2 @@ -240,11 +226,13 @@ int main(int argc, char **argv) { } // end iVoid2 } // end match finding + printf(" Sorting matches...\n"); for (iVoid1 = 0; iVoid1 < catalog1.numVoids; iVoid1++) { sortMatches(catalog1.voids[iVoid1].matches); } // count up significant matches + printf(" Categorizing matches...\n"); for (iVoid1 = 0; iVoid1 < catalog1.numVoids; iVoid1++) { closestMatchDist = 0.; for (iMatch = 0; iMatch < catalog1.voids[iVoid1].matches.size(); iMatch++) { @@ -257,12 +245,12 @@ int main(int argc, char **argv) { } // output summary + printf(" Output...\n"); std::string filename; filename = string(args.outfile_arg); - filename = filename.append("_summary.out"); + filename = filename.append("summary.out"); fp = fopen(filename.c_str(), "w"); - //fp = fopen(args.outfile_arg, "w"); - fprintf(fp, "# void ID, radius, radius ratio, common volume ratio, relative dist, num matches, num significant matches\n"); + fprintf(fp, "# void ID, radius, radius ratio, common volume ratio, common volume ratio 2, relative dist, num matches, num significant matches\n"); for (iVoid1 = 0; iVoid1 < catalog1.numVoids; iVoid1++) { int voidID = catalog1.voids[iVoid1].voidID; if (catalog1.voids[iVoid1].numMatches > 0) { @@ -272,27 +260,31 @@ int main(int argc, char **argv) { commonVolRatio = catalog1.voids[iVoid1].matches[0].commonVol / //catalog1.voids[iVoid1].numPart; catalog1.voids[iVoid1].vol; + float volRatio = catalog1.voids[iVoid1].matches[0].commonVol / + catalog2.voids[iVoid2].vol; rdist = catalog1.voids[iVoid1].matches[0].dist; rdist /= catalog1.voids[iVoid1].radius; - fprintf(fp, "%d %.2f %.2f %.2f %.2f %d %d\n", voidID, + fprintf(fp, "%d %.2f %.2f %.2f %.2f %.2f %d %d\n", voidID, catalog1.voids[iVoid1].radiusMpc, rRatio, commonVolRatio, + volRatio, rdist, catalog1.voids[iVoid1].numMatches, catalog1.voids[iVoid1].numBigMatches); } else { - fprintf(fp, "%d %f 0.0 0.0 0.0 0 0\n", voidID, - catalog1.voids[iVoid1].radius); + fprintf(fp, "%d %.2f 0.0 0.0 0.0 0.0 0 0\n", voidID, + catalog1.voids[iVoid1].radiusMpc); } } // end printing fclose(fp); // output detail + printf(" Output detail...\n"); filename = string(args.outfile_arg); - filename = filename.append("_detail.out"); + filename = filename.append("detail.out"); fp = fopen(filename.c_str(), "w"); int MAX_OUT = 10; fprintf(fp, "# void ID, match common vol\n"); @@ -300,14 +292,13 @@ int main(int argc, char **argv) { int voidID = catalog1.voids[iVoid1].voidID; fprintf(fp,"%d: ", voidID); for (iMatch = 0; iMatch < MAX_OUT; iMatch++) { - - if (iMatch < catalog1.voids[iVoid].matches.size()) { + if (iMatch < catalog1.voids[iVoid1].matches.size()) { commonVolRatio = catalog1.voids[iVoid1].matches[iMatch].commonVol / //catalog1.voids[iVoid1].numPart; catalog1.voids[iVoid1].vol; - fprintf(fp, "%.2f ", commonVolRatio); - + fprintf(fp, "%.3f ", catalog1.voids[iVoid1].matches[iMatch].dist); + //fprintf(fp, "%.2f ", commonVolRatio); } else { fprintf(fp, "0.00 "); } @@ -443,10 +434,6 @@ void loadCatalog(const char *partFile, const char *volFile, catalog.voids[i].voidProb = voidProb; catalog.voids[i].radius = pow(voidVol/catalog.numPartTot*3./4./M_PI, 1./3.); - //catalog.voids[i].biggestMatchID = -1; - //catalog.voids[i].biggestMatchVol = 0; - //catalog.voids[i].closestMatchID = -1; - //catalog.voids[i].closestMatchDist = 1.e99; catalog.voids[i].numMatches = 0; catalog.voids[i].numBigMatches = 0; @@ -548,14 +535,15 @@ void sortMatches(std::vector& matches) { MATCHPROPS tempMatch; bool swapped; - if (matches.size() == 1) return; + if (matches.size() <= 1) return; - swapped = false; - while (!swapped) { + swapped = true; + while (swapped) { swapped = false; for (int iMatch = 0; iMatch < matches.size() - 1; iMatch++) { - if (matches[iMatch].commonVol > matches[iMatch+1].commonVol) { - tempMatch = matches[iMatch]; + if (matches[iMatch].dist > matches[iMatch+1].dist) { + //if (matches[iMatch].commonVol < matches[iMatch+1].commonVol) { + tempMatch = matches[iMatch+1]; matches[iMatch+1] = matches[iMatch]; matches[iMatch] = tempMatch; swapped = true; From d4febc694247c10940187d35f9352e4b468857e1 Mon Sep 17 00:00:00 2001 From: "P.M. Sutter" Date: Thu, 20 Dec 2012 13:38:59 -0600 Subject: [PATCH 2/7] streamlined merger tree processing --- crossCompare/analysis/datasetsToAnalyze.py | 6 +++--- crossCompare/analysis/mergerTree.py | 18 +++++++++--------- 2 files changed, 12 insertions(+), 12 deletions(-) diff --git a/crossCompare/analysis/datasetsToAnalyze.py b/crossCompare/analysis/datasetsToAnalyze.py index 82cf9ac..88452f6 100755 --- a/crossCompare/analysis/datasetsToAnalyze.py +++ b/crossCompare/analysis/datasetsToAnalyze.py @@ -2,14 +2,14 @@ workDir = "/home/psutter2/workspace/Voids/" -figDir = "./figs" -dataDir = "./data" +dataDir = "/home/psutter2/workspace/Voids/multidark/crossCompare/mergerTree/" CTOOLS_PATH = "../../c_tools/" +baseSampleDir = "multidark/md_ss0.000175/sample_md_ss0.000175_z0.56_d00/" + sampleDirList = [ - "multidark/md_ss0.000175/sample_md_ss0.000175_z0.56_d00/", "multidark/md_ss0.0004/sample_md_ss0.0004_z0.56_d00/", ] diff --git a/crossCompare/analysis/mergerTree.py b/crossCompare/analysis/mergerTree.py index 47a4179..89c5e13 100755 --- a/crossCompare/analysis/mergerTree.py +++ b/crossCompare/analysis/mergerTree.py @@ -30,30 +30,30 @@ if not os.access(filename, os.F_OK): parms = imp.load_source("name", filename) globals().update(vars(parms)) -if not os.access(figDir, os.F_OK): - os.makedirs(figDir) +if not os.access(dataDir, os.F_OK): + os.makedirs(dataDir) outFileName = dataDir + "/" + dataNameBase #+ ".dat" +with open(workDir+baseSampleDir+"/sample_info.dat", 'rb') as input: + baseSample = pickle.load(input) + for (iSample, sampleDir) in enumerate(sampleDirList): - if iSample == 0: continue with open(workDir+sampleDir+"/sample_info.dat", 'rb') as input: sample = pickle.load(input) - with open(workDir+sampleDirList[0]+"/sample_info.dat", 'rb') as input: - baseSample = pickle.load(input) - - print " Working with", sample.fullName, "..." + print " Working with", sample.fullName, "...", sampleName = sample.fullName binPath = CTOOLS_PATH+"/analysis/voidOverlap" logFile = os.getcwd()+"/mergerTree.log" - stepOutputFileName = outFileName + "_" + sampleName + "_" + stepOutputFileName = outFileName + "_" + baseSample.fullName + "_" + \ + sampleName + "_" #stepOutputFileName = os.getcwd()+"/data/overlap_" - launchVoidOverlap(baseSample, sample, workDir+sampleDirList[0], + launchVoidOverlap(baseSample, sample, workDir+baseSampleDir, workDir+sampleDir, binPath, thisDataPortion="central", logFile=logFile, continueRun=False, workDir=workDir, From a7cdb807047b7ca217bdaaa04057c0f2cf31eef1 Mon Sep 17 00:00:00 2001 From: "P.M. Sutter" Date: Sun, 23 Dec 2012 16:38:54 -0600 Subject: [PATCH 3/7] added observation flag in info file; stack voids now shifts particles based on redshift of subsample --- c_tools/libzobov/particleInfo.cpp | 10 ++++++++++ c_tools/mock/generateFromCatalog.cpp | 1 + c_tools/mock/generateMock.cpp | 1 + 3 files changed, 12 insertions(+) diff --git a/c_tools/libzobov/particleInfo.cpp b/c_tools/libzobov/particleInfo.cpp index 9711db6..fa6f467 100644 --- a/c_tools/libzobov/particleInfo.cpp +++ b/c_tools/libzobov/particleInfo.cpp @@ -10,6 +10,7 @@ bool loadParticleInfo(ParticleInfo& info, const std::string& extra_info) { int numpart; + int isObservation; NcFile f_info(extra_info.c_str()); @@ -23,6 +24,7 @@ bool loadParticleInfo(ParticleInfo& info, info.ranges[2][0] = f_info.get_att("range_z_min")->as_double(0); info.ranges[2][1] = f_info.get_att("range_z_max")->as_double(0); info.mask_index = f_info.get_att("mask_index")->as_int(0); //PMS + isObservation = f_info.get_att("is_observation")->as_int(0); //PMS for (int i = 0; i < 3; i++) info.length[i] = info.ranges[i][1] - info.ranges[i][0]; @@ -59,6 +61,14 @@ bool loadParticleInfo(ParticleInfo& info, for (int i = 0; i < numpart; i++) info.particles[i].z = mul*f.readReal32(); f.endCheckpoint(); + + if (!isObservation) { + for (int i = 0; i < numpart; i++) { + info.particles[i].x += info.ranges[0][0]; + info.particles[i].y += info.ranges[1][0]; + info.particles[i].z += info.ranges[2][0]; + } + } } catch (const NoSuchFileException& e) { diff --git a/c_tools/mock/generateFromCatalog.cpp b/c_tools/mock/generateFromCatalog.cpp index d5a0aca..54cbf87 100644 --- a/c_tools/mock/generateFromCatalog.cpp +++ b/c_tools/mock/generateFromCatalog.cpp @@ -466,6 +466,7 @@ void saveForZobov(ParticleData& pdata, const string& fname, const string& paramn fp.add_att("range_z_min", -Lmax/100.); fp.add_att("range_z_max", Lmax/100.); fp.add_att("mask_index", pdata.mask_index); // PMS + fp.add_att("is_observation", 1); // PMS int nOutputPart = pdata.mask_index; //int nOutputPart = pdata.pos.size(); diff --git a/c_tools/mock/generateMock.cpp b/c_tools/mock/generateMock.cpp index a7830dd..fe21928 100644 --- a/c_tools/mock/generateMock.cpp +++ b/c_tools/mock/generateMock.cpp @@ -338,6 +338,7 @@ void saveBox(SimuData *&boxed, const std::string& outbox) f.add_att("range_z_min", ranges[4]); f.add_att("range_z_max", ranges[5]); f.add_att("mask_index", -1); + f.add_att("is_observation", 0); NcDim *NumPart_dim = f.add_dim("numpart_dim", boxed->NumPart); NcDim *NumSnap_dim = f.add_dim("numsnap_dim", num_snapshots); From 481da6edd0dd0cc03276eb1821416257626794c3 Mon Sep 17 00:00:00 2001 From: "P.M. Sutter" Date: Wed, 16 Jan 2013 14:06:36 -0600 Subject: [PATCH 4/7] fixed bug in barycenter calculation --- c_tools/stacking/pruneVoids.cpp | 75 +++++++++++++++++++++++++++------ 1 file changed, 61 insertions(+), 14 deletions(-) diff --git a/c_tools/stacking/pruneVoids.cpp b/c_tools/stacking/pruneVoids.cpp index cd88462..b0c284c 100644 --- a/c_tools/stacking/pruneVoids.cpp +++ b/c_tools/stacking/pruneVoids.cpp @@ -103,6 +103,9 @@ int main(int argc, char **argv) { args_info.periodic_arg); // check for periodic box + periodicX = 0; + periodicY = 0; + periodicZ = 0; if (!args_info.isObservation_flag) { if ( strchr(args_info.periodic_arg, 'x') != NULL) { periodicX = 1; @@ -143,9 +146,9 @@ int main(int argc, char **argv) { temp = (float *) malloc(numPartTot * sizeof(float)); volNorm = numPartTot/(boxLen[0]*boxLen[1]*boxLen[2]); - printf("VOL NORM = %f\n", volNorm); + printf(" VOL NORM = %f\n", volNorm); - printf("CENTRAL DEN = %f\n", args_info.maxCentralDen_arg); + printf(" CENTRAL DEN = %f\n", args_info.maxCentralDen_arg); fread(&dummy, 1, 4, fp); fread(temp, numPartTot, 4, fp); @@ -311,13 +314,16 @@ int main(int argc, char **argv) { voids[iVoid].barycenter[2] = 0.; for (p = 0; p < voids[iVoid].numPart; p++) { - dist[0] = fabs(voidPart[p].x - voids[iVoid].center[0]); - dist[1] = fabs(voidPart[p].y - voids[iVoid].center[1]); - dist[2] = fabs(voidPart[p].z - voids[iVoid].center[2]); + dist[0] = voidPart[p].x - voids[iVoid].center[0]; + dist[1] = voidPart[p].y - voids[iVoid].center[1]; + dist[2] = voidPart[p].z - voids[iVoid].center[2]; - if (periodicX) dist[0] = fmin(dist[0], boxLen[0]-dist[0]); - if (periodicY) dist[1] = fmin(dist[1], boxLen[1]-dist[1]); - if (periodicZ) dist[2] = fmin(dist[2], boxLen[2]-dist[2]); + if (periodicX && fabs(dist[0]) > boxLen[0]/2.) + dist[0] = dist[0] - copysign(boxLen[0], dist[0]); + if (periodicY && fabs(dist[1]) > boxLen[1]/2.) + dist[1] = dist[1] - copysign(boxLen[1], dist[1]); + if (periodicZ && fabs(dist[2]) > boxLen[2]/2.) + dist[2] = dist[2] - copysign(boxLen[2], dist[2]); voids[iVoid].barycenter[0] += voidPart[p].vol*(dist[0]); voids[iVoid].barycenter[1] += voidPart[p].vol*(dist[1]); @@ -331,12 +337,25 @@ int main(int argc, char **argv) { voids[iVoid].barycenter[1] += voids[iVoid].center[1]; voids[iVoid].barycenter[2] += voids[iVoid].center[2]; - if (periodicX) - voids[iVoid].barycenter[0] = fmod(voids[iVoid].barycenter[0], boxLen[0]); - if (periodicY) - voids[iVoid].barycenter[1] = fmod(voids[iVoid].barycenter[1], boxLen[1]); - if (periodicZ) - voids[iVoid].barycenter[2] = fmod(voids[iVoid].barycenter[2], boxLen[2]); + if (periodicX) { + if (voids[iVoid].barycenter[0] > boxLen[0]) + voids[iVoid].barycenter[0] = voids[iVoid].barycenter[0] - boxLen[0]; + if (voids[iVoid].barycenter[0] < 0) + voids[iVoid].barycenter[0] = boxLen[0] - voids[iVoid].barycenter[0]; + } + if (periodicY) { + if (voids[iVoid].barycenter[1] > boxLen[1]) + voids[iVoid].barycenter[1] = voids[iVoid].barycenter[1] - boxLen[1]; + if (voids[iVoid].barycenter[1] < 1) + voids[iVoid].barycenter[1] = boxLen[1] - voids[iVoid].barycenter[1]; + } + if (periodicZ) { + if (voids[iVoid].barycenter[2] > boxLen[2]) + voids[iVoid].barycenter[2] = voids[iVoid].barycenter[2] - boxLen[2]; + if (voids[iVoid].barycenter[2] < 2) + voids[iVoid].barycenter[2] = boxLen[2] - voids[iVoid].barycenter[2]; + } + // compute central density centralRad = voids[iVoid].radius/args_info.centralRadFrac_arg; @@ -450,6 +469,11 @@ int main(int argc, char **argv) { voids[iVoid].nearestEdge = nearestEdge; } // iVoid + int numWrong = 0; + int numHighDen = 0; + int numEdge = 0; + int numTooSmall = 0; + printf(" Picking winners and losers...\n"); for (iVoid = 0; iVoid < numVoids; iVoid++) { voids[iVoid].accepted = 1; @@ -462,36 +486,43 @@ int main(int argc, char **argv) { if (voids[iVoid].centralDen > args_info.maxCentralDen_arg) { voids[iVoid].accepted = -1; + numHighDen++; } // toss out voids that are obviously wrong if (voids[iVoid].densCon > 1.e3) { voids[iVoid].accepted = -4; + numWrong++; } if (strcmp(args_info.dataPortion_arg, "edge") == 0 && tolerance*voids[iVoid].maxRadius < voids[iVoid].nearestMock) { voids[iVoid].accepted = -3; + numEdge++; } if (strcmp(args_info.dataPortion_arg, "central") == 0 && tolerance*voids[iVoid].maxRadius > voids[iVoid].nearestMock) { voids[iVoid].accepted = -3; + numEdge++; } if (voids[iVoid].radius < args_info.rMin_arg) { voids[iVoid].accepted = -2; + numTooSmall++; } // *always* clean out near edges since there are no mocks there if (tolerance*voids[iVoid].maxRadius > voids[iVoid].nearestEdge) { voids[iVoid].accepted = -3; + numEdge++; } // assume the lower z-boundary is "soft" in observations if (args_info.isObservation_flag && voids[iVoid].redshift < args_info.zMin_arg) { voids[iVoid].accepted = -3; + numEdge++; } } @@ -501,6 +532,10 @@ int main(int argc, char **argv) { } printf(" Number kept: %d (out of %d)\n", numKept, numVoids); + printf(" Rejected %d near the edge\n", numEdge); + printf(" Rejected %d too small\n", numTooSmall); + printf(" Rejected %d obviously bad\n", numWrong); + printf(" Rejected %d too high central density\n", numHighDen); printf(" Output...\n"); fp = fopen(args_info.output_arg, "w"); @@ -531,6 +566,10 @@ int main(int argc, char **argv) { fprintf(fpBarycenter, "%d %e %e %e\n", voids[iVoid].voidID, +// TEST + //voids[iVoid].center[0], + //voids[iVoid].center[1], + //voids[iVoid].center[2]); voids[iVoid].barycenter[0], voids[iVoid].barycenter[1], voids[iVoid].barycenter[2]); @@ -540,11 +579,19 @@ int main(int argc, char **argv) { voids[iVoid].nearestMock); double outCenter[3]; +// TEST + //outCenter[0] = voids[iVoid].center[0]; + //outCenter[1] = voids[iVoid].center[1]; + //outCenter[2] = voids[iVoid].center[2]; outCenter[0] = voids[iVoid].barycenter[0]; outCenter[1] = voids[iVoid].barycenter[1]; outCenter[2] = voids[iVoid].barycenter[2]; if (args_info.isObservation_flag) { +// TEST + //outCenter[0] = (voids[iVoid].center[0]-boxLen[0]/2.)*100.; + //outCenter[1] = (voids[iVoid].center[1]-boxLen[1]/2.)*100.; + //outCenter[2] = (voids[iVoid].center[2]-boxLen[2]/2.)*100.; outCenter[0] = (voids[iVoid].barycenter[0]-boxLen[0]/2.)*100.; outCenter[1] = (voids[iVoid].barycenter[1]-boxLen[1]/2.)*100.; outCenter[2] = (voids[iVoid].barycenter[2]-boxLen[2]/2.)*100.; From 4338a08f447210de97ecdcbf178758744b8a7ea1 Mon Sep 17 00:00:00 2001 From: nhamaus Date: Thu, 17 Jan 2013 15:10:25 +0100 Subject: [PATCH 5/7] fixed particle selection problem in generateMock --- c_tools/mock/generateMock.cpp | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/c_tools/mock/generateMock.cpp b/c_tools/mock/generateMock.cpp index ab51315..ad334e9 100644 --- a/c_tools/mock/generateMock.cpp +++ b/c_tools/mock/generateMock.cpp @@ -221,7 +221,12 @@ void generateOutput(SimuData *data, int axis, // cleared. That way new particles can be appended if this is a multi-file snapshot. void selectBox(SimuData *simu, std::vector& targets, generateMock_info& args_info) { - float subsample = args_info.subsample_given ? args_info.subsample_arg : 1.0; + float subsample; + if (args_info.subsample_given) { + subsample = args_info.subsample_arg; + } else { + subsample = 1.0; + } double ranges[3][2] = { { args_info.rangeX_min_arg, args_info.rangeX_max_arg }, { args_info.rangeY_min_arg, args_info.rangeY_max_arg }, From ea58ff2b837d0346bad0cae3e863fadec841f64c Mon Sep 17 00:00:00 2001 From: "P.M. Sutter" Date: Thu, 17 Jan 2013 09:31:13 -0600 Subject: [PATCH 6/7] made default profile bin size 'auto' --- .../pipeline_source/prepareCatalogs.in.py | 24 ++++++++++++------- 1 file changed, 16 insertions(+), 8 deletions(-) diff --git a/python_tools/pipeline_source/prepareCatalogs.in.py b/python_tools/pipeline_source/prepareCatalogs.in.py index fc7c927..cb0cc63 100755 --- a/python_tools/pipeline_source/prepareCatalogs.in.py +++ b/python_tools/pipeline_source/prepareCatalogs.in.py @@ -79,7 +79,7 @@ startCatalogStage = 1 endCatalogStage = 4 startAPStage = 1 -endAPStage = 7 +endAPStage = 1 ZOBOV_PATH = "@CMAKE_BINARY_DIR@/zobov/" CTOOLS_PATH = "@CMAKE_BINARY_DIR@/c_tools/" @@ -124,7 +124,7 @@ newSample = Sample(dataFile = "{dataFile}", zBoundaryMpc = ({zMinMpc}, {zMaxMpc}), omegaM = {omegaM}, minVoidRadius = {minRadius}, - profileBinSize = 1.0, + profileBinSize = "auto", includeInHubble = True, partOfCombo = False, isCombo = False, @@ -135,12 +135,20 @@ newSample = Sample(dataFile = "{dataFile}", useLightCone = {useLightCone}, subsample = {subsample}) dataSampleList.append(newSample) -newSample.addStack({zMin}, {zMax}, 2*{minRadius} , 2*{minRadius}+2, True, False) -newSample.addStack({zMin}, {zMax}, 2*{minRadius} , 2*{minRadius}+4, True, False) -newSample.addStack({zMin}, {zMax}, 2*{minRadius}+2, 2*{minRadius}+6, True, False) -newSample.addStack({zMin}, {zMax}, 2*{minRadius}+6, 2*{minRadius}+10, True, False) -newSample.addStack({zMin}, {zMax}, 2*{minRadius}+10, 2*{minRadius}+18, True, False) -newSample.addStack({zMin}, {zMax}, 2*{minRadius}+18, 2*{minRadius}+24, True, False) +newSample.addStack(0.0, 5.0, 20, 25, False, False) +newSample.addStack(0.0, 5.0, 30, 35, False, False) +newSample.addStack(0.0, 5.0, 40, 45, False, False) +newSample.addStack(0.0, 5.0, 50, 55, False, False) +newSample.addStack(0.0, 5.0, 60, 65, False, False) +newSample.addStack(0.0, 5.0, 70, 75, False, False) +newSample.addStack(0.0, 5.0, 80, 85, False, False) +newSample.addStack(0.0, 5.0, 90, 95, False, False) +#newSample.addStack({zMin}, {zMax}, 2*{minRadius} , 2*{minRadius}+2, True, False) +#newSample.addStack({zMin}, {zMax}, 2*{minRadius} , 2*{minRadius}+4, True, False) +#newSample.addStack({zMin}, {zMax}, 2*{minRadius}+2, 2*{minRadius}+6, True, False) +#newSample.addStack({zMin}, {zMax}, 2*{minRadius}+6, 2*{minRadius}+10, True, False) +#newSample.addStack({zMin}, {zMax}, 2*{minRadius}+10, 2*{minRadius}+18, True, False) +#newSample.addStack({zMin}, {zMax}, 2*{minRadius}+18, 2*{minRadius}+24, True, False) """ for (iFile, redshift) in enumerate(redshifts): fileNum = fileNums[iFile] From ae9701e99c8e762c142323fd68aabcdafadf551a Mon Sep 17 00:00:00 2001 From: "P.M. Sutter" Date: Fri, 18 Jan 2013 09:56:31 -0600 Subject: [PATCH 7/7] replaced void shape fitter with rudimentary moment of inertia calculation --- c_tools/stacking/pruneVoids.cpp | 2 +- .../apTools/profiles/__init__.py | 1 + .../void_python_tools/backend/launchers.py | 48 +++++++++++-------- 3 files changed, 30 insertions(+), 21 deletions(-) diff --git a/c_tools/stacking/pruneVoids.cpp b/c_tools/stacking/pruneVoids.cpp index b0c284c..37f39a3 100644 --- a/c_tools/stacking/pruneVoids.cpp +++ b/c_tools/stacking/pruneVoids.cpp @@ -490,7 +490,7 @@ int main(int argc, char **argv) { } // toss out voids that are obviously wrong - if (voids[iVoid].densCon > 1.e3) { + if (voids[iVoid].densCon > 1.e4) { voids[iVoid].accepted = -4; numWrong++; } diff --git a/python_tools/void_python_tools/apTools/profiles/__init__.py b/python_tools/void_python_tools/apTools/profiles/__init__.py index b05e408..0f04a3e 100644 --- a/python_tools/void_python_tools/apTools/profiles/__init__.py +++ b/python_tools/void_python_tools/apTools/profiles/__init__.py @@ -1,6 +1,7 @@ from build import * from draw import * from fit import * +from inertia import * from mcmc import * from generateExpFigure import * from getSurveyProps import * diff --git a/python_tools/void_python_tools/backend/launchers.py b/python_tools/void_python_tools/backend/launchers.py index 45c117a..28cd70c 100755 --- a/python_tools/void_python_tools/backend/launchers.py +++ b/python_tools/void_python_tools/backend/launchers.py @@ -314,7 +314,8 @@ def launchPrune(sample, binPath, thisDataPortion=None, def launchVoidOverlap(sample1, sample2, sample1Dir, sample2Dir, binPath, thisDataPortion=None, logFile=None, workDir=None, - continueRun=None, outputFile=None): + continueRun=None, outputFile=None, + matchMethod=None): sampleName1 = sample1.fullName sampleName2 = sample2.fullName @@ -358,7 +359,7 @@ def launchVoidOverlap(sample1, sample2, sample1Dir, sample2Dir, cmd += " --zonePartFile2=" + sample2Dir+"/voidPart_" + \ str(sampleName2)+".dat" - cmd += " --useID" + if matchMethod == "useID": cmd += " --useID" cmd += periodicLine cmd += " --outfile=" + outputFile cmd += " &> " + logFile @@ -600,13 +601,18 @@ def launchStack(sample, stack, binPath, thisDataPortion=None, logDir=None, os.system("mv %s %s" % ("tree.data", treeFile)) os.system("mv %s %s" % ("void_indexes.txt", voidDir+"/")) - os.system("mv %s %s" % ("posx.nc", voidDir+"/posx.nc")) - os.system("mv %s %s" % ("posy.nc", voidDir+"/posy.nc")) - os.system("mv %s %s" % ("posz.nc", voidDir+"/posz.nc")) - os.system("mv %s %s" % ("redshifts.nc", voidDir+"/redshifts.nc")) + os.system("mv %s %s" % ("posx.nc", voidDir+"/")) + os.system("mv %s %s" % ("posy.nc", voidDir+"/")) + os.system("mv %s %s" % ("posz.nc", voidDir+"/")) + os.system("mv %s %s" % ("z_void_indexes.txt", voidDir+"/")) + os.system("mv %s %s" % ("z_posx.nc", voidDir+"/")) + os.system("mv %s %s" % ("z_posy.nc", voidDir+"/")) + os.system("mv %s %s" % ("z_posz.nc", voidDir+"/")) + os.system("mv %s %s" % ("redshifts.nc", voidDir+"/")) os.system("mv %s %s" % ("indexes.nc", voidDir+"/")) os.system("mv %s %s" % ("kdtree_stackvoids.dat", voidDir+"/")) os.system("mv %s %s" % ("centers.txt", voidDir+"/")) + os.system("mv %s %s" % ("z_centers.txt", voidDir+"/")) os.system("mv %s %s" % ("sky_positions.txt", voidDir+"/")) os.system("mv %s %s" % ("check.txt", voidDir+"/")) os.system("mv %s %s" % ("tracer.txt", voidDir+"/")) @@ -899,22 +905,24 @@ def launchFit(sample, stack, logFile=None, voidDir=None, figDir=None, while badChain: Rexpect = (stack.rMin+stack.rMax)/2 Rtruncate = stack.rMin*3. + 1 # TEST - if sample.dataType == "observation": - ret,fits,args = vp.fit_ellipticity(voidDir,Rbase=Rexpect, - Niter=300000, - Nburn=100000, - Rextracut=Rtruncate) - else: - ret,fits,args = vp.fit_ellipticity(voidDir,Rbase=Rexpect, - Niter=300000, - Nburn=100000, - Rextracut=Rtruncate) - badChain = (args[0][0] > 0.5 or args[0][1] > stack.rMax or \ - args[0][2] > stack.rMax) and \ - (ntries < maxtries) + #if sample.dataType == "observation": + # ret,fits,args = vp.fit_ellipticity(voidDir,Rbase=Rexpect, + # Niter=300000, + # Nburn=100000, + # Rextracut=Rtruncate) + #else: + # ret,fits,args = vp.fit_ellipticity(voidDir,Rbase=Rexpect, + # Niter=300000, + # Nburn=100000, + # Rextracut=Rtruncate) + #badChain = (args[0][0] > 0.5 or args[0][1] > stack.rMax or \ + # args[0][2] > stack.rMax) and \ + # (ntries < maxtries) + ret,fits,args = vp.compute_inertia(voidDir, stack.rMax) + badChain = False ntries += 1 - np.save(voidDir+"/chain.npy", ret) + #np.save(voidDir+"/chain.npy", ret) np.savetxt(voidDir+"/fits.out", fits) plotTitle = "Sample: "+sample.nickName+\