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Merge branch 'master' of ssh://bitbucket.org/cosmicvoids/void_identification

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This commit is contained in:
Guilhem Lavaux 2013-01-19 12:17:02 -05:00
commit 361ab5b617
10 changed files with 192 additions and 123 deletions
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122
c_tools/analysis/voidOverlap.cpp
View file

@ -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<MATCHPROPS>& 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;

10
c_tools/libzobov/particleInfo.cpp
View file

@ -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)
{

1
c_tools/mock/generateFromCatalog.cpp
View file

@ -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();

8
c_tools/mock/generateMock.cpp
View file

@ -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<long>& 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 },
@ -338,6 +343,7 @@ 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);

77
c_tools/stacking/pruneVoids.cpp
View file

@ -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) {
if (voids[iVoid].densCon > 1.e4) {
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.;