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carried boundary flags all the way through to pruning; cleaned up pruning routines

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This commit is contained in:
Paul M. Sutter 2024-06-06 20:26:47 +02:00
parent dd181da42a
commit a45eca0b6e
5 changed files with 124 additions and 139 deletions
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144
c_source/pruning/pruneVoids.cpp
View file

@ -59,6 +59,7 @@ typedef struct partStruct {
float x, y, z, vol;
int nadj, ncnt;
int *adj;
int edgeFlag;
} PART;
typedef struct zoneStruct {
@ -390,7 +391,7 @@ int main(int argc, char **argv) {
}
}
// and finally volumes
// and volumes
printf(" Loading particle volumes...\n");
fp = fopen(args.partVol_arg, "r");
fread(&mask_index, 1, 4, fp);
@ -404,7 +405,16 @@ int main(int argc, char **argv) {
}
fclose(fp);
/*
// and finally edge flag info
printf(" Loading particle edge flags...\n");
fp = fopen(args.partEdge_arg, "r");
for (p = 0; p < mask_index; p++) {
fscanf(fp, "%d", &part[p].edgeFlag);
//printf("EDGE VALUE %d\n", part[p].edgeFlag);
}
fclose(fp);
/* this was used for testing at one point
// and finally finally adjacencies
printf(" Loading particle adjacencies...\n");
fp = fopen(args.partAdj_arg, "r");
@ -458,13 +468,11 @@ int main(int argc, char **argv) {
interval = 1.*(clock4 - clock3)/CLOCKS_PER_SEC;
printf(" Read voids (%.2f sec)...\n", interval);
// load voids *again* using Guilhem's code so we can get tree
// load voids *again* using Guilhem's code so we can get tree information
clock3 = clock();
//if (!args.isObservation_flag) {
printf(" Re-loading voids and building tree..\n");
ZobovRep zobovCat;
if (!loadZobov(args.voidDesc_arg, args.zone2Part_arg,
args.void2Zone_arg,
if (!loadZobov(args.voidDesc_arg, args.zone2Part_arg, args.void2Zone_arg,
0, zobovCat)) {
printf("Error loading catalog!\n");
return -1;
@ -488,25 +496,23 @@ int main(int argc, char **argv) {
}
voids[iVoid].level = level;
}
//} // end re-load
clock4 = clock();
interval = 1.*(clock4 - clock3)/CLOCKS_PER_SEC;
printf(" Re-read voids (%.2f sec)...\n", interval);
// check boundaries
printf(" Computing void properties...\n");
// allocate space for a particle buffer
maxNumPart = 0;
for (iVoid = 0; iVoid < numVoids; iVoid++) {
if (voids[iVoid].numPart > maxNumPart) maxNumPart = voids[iVoid].numPart;
}
voidPart = (PART *) malloc(maxNumPart * sizeof(PART));
// main processing of each void
for (iVoid = 0; iVoid < numVoids; iVoid++) {
voidID = voids[iVoid].voidID;
printf(" DOING %d (of %d) %d %d %f\n", iVoid+1, numVoids, voidID,
printf(" Working on void %d (of %d) %d %d %f\n",iVoid+1, numVoids, voidID,
voids[iVoid].numPart,
voids[iVoid].radius);
@ -514,6 +520,8 @@ int main(int argc, char **argv) {
voids[iVoid].center[1] = part[voids[iVoid].coreParticle].y;
voids[iVoid].center[2] = part[voids[iVoid].coreParticle].z;
voids[iVoid].voidType = CENTRAL_VOID;
// first load up particles into a buffer
clock3 = clock();
i = 0;
@ -523,6 +531,7 @@ int main(int argc, char **argv) {
for (p = 0; p < zones2Parts[zoneID].numPart; p++) {
partID = zones2Parts[zoneID].partIDs[p];
// something went haywire
if (partID > mask_index ||
(part[partID].vol < 1.e-27 && part[partID].vol > 0.)) {
printf("BAD PART!? %d %d %e", partID, mask_index, part[partID].vol);
@ -533,6 +542,12 @@ int main(int argc, char **argv) {
voidPart[i].y = part[partID].y;
voidPart[i].z = part[partID].z;
voidPart[i].vol = part[partID].vol;
voidPart[i].edgeFlag = part[partID].edgeFlag;
// check for edge contamination
if (voidPart[i].edgeFlag > 0) {
voids[iVoid].voidType = EDGE_VOID;
}
/*
// testing for edge contamination
@ -549,7 +564,7 @@ int main(int argc, char **argv) {
*/
i++;
}
}
} // loading particles
clock4 = clock();
interval = 1.*(clock4 - clock3)/CLOCKS_PER_SEC;
@ -632,55 +647,10 @@ int main(int argc, char **argv) {
interval = 1.*(clock4 - clock3)/CLOCKS_PER_SEC;
//printf(" %.2f for central density\n", interval);
//coreParticle = voids[iVoid].coreParticle;
//voids[iVoid].rescaledCoreDens = voids[iVoid].coreDens*(pow(1.*mockIndex/numPartTot,3));
// // compute distance from core to nearest mock
// minDist = 1.e99;
// for (p = mockIndex; p < numPartTot; p++) {
// dist[0] = part[coreParticle].x - part[p].x;
// dist[1] = part[coreParticle].y - part[p].y;
// dist[2] = part[coreParticle].z - part[p].z;
//
// dist2 = pow(dist[0],2) + pow(dist[1],2) + pow(dist[2],2);
// if (dist2 < minDist) minDist = dist2;
// }
// voids[iVoid].nearestMockFromCore = sqrt(minDist);
//
// // compute distance from core to nearest mock
// minDist = 1.e99;
// for (p = 0; p < mockIndex; p++) {
// dist[0] = part[coreParticle].x - part[p].x;
// dist[1] = part[coreParticle].y - part[p].y;
// dist[2] = part[coreParticle].z - part[p].z;
//
// dist2 = pow(dist[0],2) + pow(dist[1],2) + pow(dist[2],2);
// if (dist2 < minDist && dist2 > 1.e-10) minDist = dist2;
// }
// voids[iVoid].nearestGalFromCore = sqrt(minDist);
// compute maximum extent
/*
if (args.isObservation_flag) {
maxDist = 0.;
for (p = 0; p < voids[iVoid].numPart; p++) {
for (p2 = p; p2 < voids[iVoid].numPart; p2++) {
dist[0] = voidPart[p].x - voidPart[p2].x;
dist[1] = voidPart[p].y - voidPart[p2].y;
dist[2] = voidPart[p].z - voidPart[p2].z;
dist2 = pow(dist[0],2) + pow(dist[1],2) + pow(dist[2],2);
if (dist2 > maxDist) maxDist = dist2;
}
}
voids[iVoid].maxRadius = sqrt(maxDist)/2.;
} else {
*/
// compute maximum extent of void
clock3 = clock();
maxDist = 0.;
for (p = 0; p < voids[iVoid].numPart; p++) {
dist[0] = fabs(voidPart[p].x - voids[iVoid].macrocenter[0]);
dist[1] = fabs(voidPart[p].y - voids[iVoid].macrocenter[1]);
dist[2] = fabs(voidPart[p].z - voids[iVoid].macrocenter[2]);
@ -696,11 +666,11 @@ int main(int argc, char **argv) {
clock4 = clock();
interval = 1.*(clock4 - clock3)/CLOCKS_PER_SEC;
//printf(" %.2f for maximum extent\n", interval);
// }
// compute distance from center to nearest mock boundary particle
// (with new boundary handling this will go away)
clock3 = clock();
if (args.isObservation_flag) {
// compute distance from center to nearest mock
minDist = 1.e99;
for (p = mockIndex; p < numPartTot; p++) {
dist[0] = voids[iVoid].macrocenter[0] - part[p].x;
@ -727,7 +697,6 @@ int main(int argc, char **argv) {
if (args.useComoving_flag) {
redshift = gsl_interp_eval(interp, dL, redshifts,
voids[iVoid].redshiftInMpc, acc);
//printf("HELLO %e %e\n", redshift, args.zMax_arg);
nearestEdge = fabs((redshift-args.zMax_arg)*LIGHT_SPEED/100.);
voids[iVoid].redshift = redshift;
} else {
@ -828,24 +797,16 @@ int main(int argc, char **argv) {
if (gsl_vector_get(voids[iVoid].eval,i) > largest)
largest = gsl_vector_get(voids[iVoid].eval,i);
}
// TEST
voids[iVoid].ellip = 1.0 - sqrt(sqrt(fabs(smallest/largest)));
//if (a < c) ca = a/c;
//if (a >= c) ca = c/a;
//voids[iVoid].ellip = fabs(1.0 - ca);
//if (a < c) ca = a*a/(c*c);
//if (a >= c) ca = (c*c)/(a*a);
//voids[iVoid].ellip = sqrt(fabs(1.0 - ca));
clock4 = clock();
interval = 1.*(clock4 - clock3)/CLOCKS_PER_SEC;
//printf(" %.2f for ellipticity\n", interval);
} // iVoid
gsl_eigen_symmv_free(eigw);
// now filter and categorize the voids based on various criteria
int numWrong = 0;
int numHighDen = 0;
int numCentral = 0;
@ -861,15 +822,6 @@ int main(int argc, char **argv) {
voids[iVoid].accepted = 1;
}
/*
int j = 0;
for (iVoid = 0; iVoid < voids.size(); iVoid++) {
if (voids[iVoid].densCon < 1.5) {
// voids[iVoid].accepted = -4;
}
}
*/
// toss out voids that are obviously wrong
int iGood = 0;
for (iVoid = 0; iVoid < voids.size(); iVoid++) {
@ -883,6 +835,7 @@ int main(int argc, char **argv) {
voids.resize(iGood);
printf(" 1st filter: rejected %d obviously bad\n", numWrong);
// toss out voids that are too small
iGood = 0;
for (iVoid = 0; iVoid < voids.size(); iVoid++) {
if (voids[iVoid].radius < args.rMin_arg) {
@ -895,9 +848,9 @@ int main(int argc, char **argv) {
printf(" 2nd filter: rejected %d too small\n", numTooSmall);
// toss out voids near non-periodic box edges
iGood = 0;
for (iVoid = 0; iVoid < voids.size(); iVoid++) {
// *always* clean out near edges since there are no mocks there
if (tolerance*voids[iVoid].maxRadius > voids[iVoid].nearestEdge ||
tolerance*voids[iVoid].radius > voids[iVoid].nearestEdge) {
numNearZ++;
@ -908,6 +861,7 @@ int main(int argc, char **argv) {
voids.resize(iGood);
printf(" 3rd filter: rejected %d too close to high redshift boundaries\n", numNearZ);
// toss out voids that are beyond redshift boundaries
numNearZ = 0;
iGood = 0;
for (iVoid = 0; iVoid < voids.size(); iVoid++) {
@ -921,24 +875,18 @@ int main(int argc, char **argv) {
}
voids.resize(iGood);
//Maubert - Uncommented this part : to be sure that voids do not cross maximum redshift asked for in zrange
iGood = 0;
for (iVoid = 0; iVoid < voids.size(); iVoid++) {
// just in case
if (args.isObservation_flag &&
voids[iVoid].redshift > args.zMax_arg) {
if (args.isObservation_flag && voids[iVoid].redshift > args.zMax_arg) {
numNearZ++;
} else {
voids[iGood++] = voids[iVoid];
}
}
voids.resize(iGood);
// Maubert - End of Uncommented part
printf(" 4th filter: rejected %d outside redshift boundaries\n", numNearZ);
// take only top-level voids
// find top-level voids
numAreParents = 0;
iGood = 0;
for (iVoid = 0; iVoid < voids.size(); iVoid++) {
@ -950,7 +898,7 @@ int main(int argc, char **argv) {
}
}
// mark high-density voids
for (iVoid = 0; iVoid < voids.size(); iVoid++) {
if (voids[iVoid].centralDen > args.maxCentralDen_arg) {
voids[iVoid].accepted = -1;
@ -961,6 +909,17 @@ int main(int argc, char **argv) {
}
}
// count voids near survey edges
for (iVoid = 0; iVoid < voids.size(); iVoid++) {
if (voids[iVoid].voidType == CENTRAL_VOID) {
numCentral++;
} else {
numEdge++;
}
}
/*
// mark voids near survey edges
for (iVoid = 0; iVoid < voids.size(); iVoid++) {
if (tolerance*voids[iVoid].maxRadius < voids[iVoid].nearestMock) {
voids[iVoid].voidType = CENTRAL_VOID;
@ -970,6 +929,7 @@ int main(int argc, char **argv) {
numEdge++;
}
}
*/
printf(" Number kept: %d (out of %d)\n", (int) voids.size(), numVoids);
printf(" We have %d edge voids\n", numEdge);
@ -988,7 +948,6 @@ int main(int argc, char **argv) {
prefix = "";
for (int i = 0; i < 2; i++) {
dataPortion = dataPortions[i];
outputVoids(outputDir, sampleName, prefix, dataPortion,
mockIndex,
voids,
@ -999,7 +958,6 @@ int main(int argc, char **argv) {
prefix = "untrimmed_";
for (int i = 0; i < 2; i++) {
dataPortion = dataPortions[i];
outputVoids(outputDir, sampleName, prefix, dataPortion,
mockIndex,
voids,
@ -1010,7 +968,6 @@ int main(int argc, char **argv) {
prefix = "untrimmed_dencut_";
for (int i = 0; i < 2; i++) {
dataPortion = dataPortions[i];
outputVoids(outputDir, sampleName, prefix, dataPortion,
mockIndex,
voids,
@ -1020,7 +977,6 @@ int main(int argc, char **argv) {
prefix = "trimmed_nodencut_";
for (int i = 0; i < 2; i++) {
dataPortion = dataPortions[i];
outputVoids(outputDir, sampleName, prefix, dataPortion,
mockIndex,
voids,

2
c_source/pruning/pruneVoids.ggo
View file

@ -16,6 +16,8 @@ option "partVol" - "Particle volume file from ZOBOV" string required
option "partAdj" - "Adjacency file from ZOBOV" string required
option "partEdge" - "Boundary flag file" string required
option "zone2Part" - "Particle file from ZOBOV" string required
option "mockIndex" - "Beginning index of mock particles" int required

2
examples/example_observation/example_observation.py
View file

@ -30,7 +30,7 @@ continueRun = False
# 1 : extract redshift slices from data
# 2 : void extraction using zobov
# 3 : removal of small voids and voids near the edge
startCatalogStage = 1
startCatalogStage = 3
endCatalogStage = 3
basePath = os.path.dirname(os.path.abspath(__file__))

26
python_source/backend/launchers.py
View file

@ -446,6 +446,31 @@ def launchZobov(sample, binPath, outputDir=None, logDir=None, continueRun=None,
else:
volFileToUse = outputDir+"/vol_"+sampleName+".dat"
# re-weight the volumes of any edge galaxies to prevent watershed
# from spilling outside of survey region
if sample.dataType == "observation":
# read in the appropriate volume file
with open(volFileToUse, mode="rb") as File:
numPartTot = np.fromfile(File, dtype=np.int32,count=1)[0]
vols = np.fromfile(File, dtype=np.float32, count=numPartTot)
# read in the edge flag information
edgeFile = outputDir+"/galaxy_edge_flags.txt"
edgeFlags = np.loadtxt(edgeFile, dtype=np.int32)
# set edge galaxy volumes to nearly 0 (implying very high density)
vols[ edgeFlags>0 ] = 1.e-4
volFile = outputDir+"/vol_weighted_"+sampleName+".dat"
with open(volFile, mode='wb') as File:
numPartTot.astype(np.int32).tofile(File)
vols.astype(np.float32).tofile(File)
volFileToUse = outputDir+"/vol_weighted_"+sampleName+".dat"
else:
volFileToUse = outputDir+"/vol_"+sampleName+".dat"
cmd = [binPath+"/jozov2", \
outputDir+"/adj_"+sampleName+".dat", \
@ -525,6 +550,7 @@ def launchPrune(sample, binPath,
cmd += " --zone2Part=" + outputDir+"/voidPart_"+str(sampleName)+".dat"
cmd += " --partVol=" + outputDir+"/vol_"+str(sampleName)+".dat"
cmd += " --partAdj=" + outputDir+"/adj_"+str(sampleName)+".dat"
cmd += " --partEdge=" + outputDir+"galaxy_edge_flags.txt"
cmd += " --extraInfo=" + outputDir+"/zobov_slice_"+str(sampleName)+\
".par"
cmd += " --tolerance=" + str(boundaryTolerance)

9
python_source/backend/surveyTools.py
View file

@ -161,18 +161,19 @@ def findEdgeGalaxies(galFile, maskFile, edgeGalFile, edgeMaskFile,
phi, theta = convertAngle(RA, Dec)
# check the mask edges
neighbors = healpy.get_all_neighbours(nside, theta, phi)
isOnMaskEdge = any(p == 0 for p in neighbors)
ipix = healpy.ang2pix(nside, theta, phi)
neighbors = healpy.get_all_neighbours(nside, ipix)
isOnMaskEdge = any(mask[p] == 0 for p in neighbors)
# check the redshift boundaries
tol = 0.01 # TODO: made this user-adjustable
tol = 0.05 # TODO: made this user-adjustable
zbuffer = (zmax-zmin)*tol
isOnHighZEdge = (z >= zmax-zbuffer)
isOnLowZEdge = (z <= zmin+zbuffer)
print("DOING %f %f %f %f\n" % (zbuffer, z, zmax, zmin) )
if isOnMaskEdge:
edgeFile.write("1\n")
edgeMask[ipix] = 1
elif isOnHighZEdge:
edgeFile.write("2\n")
elif isOnLowZEdge: