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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.;

6
crossCompare/analysis/datasetsToAnalyze.py
View file

@ -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/",
]

18
crossCompare/analysis/mergerTree.py
View file

@ -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,

24
python_tools/pipeline_source/prepareCatalogs.in.py
View file

@ -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]

1
python_tools/void_python_tools/apTools/profiles/__init__.py
View file

@ -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 *

48
python_tools/void_python_tools/backend/launchers.py
View file

@ -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+\