guilhem_lavaux/vide_public
0
0
Fork 0
mirror of https://bitbucket.org/cosmicvoids/vide_public.git synced 2025-07-04 15:21:11 +00:00
Code Issues Projects Releases Packages Wiki Activity Actions

merged guilhem's and my updates

Browse source
This commit is contained in:
P.M. Sutter 2013-02-09 14:12:40 -06:00
commit 168ef7a0d7
11 changed files with 124 additions and 39 deletions
Download patch file Download diff file Expand all files Collapse all files

2
c_tools/libzobov/loadZobov.cpp
View file

@ -1,3 +1,4 @@
#include <cassert>
#include <string>
#include <fstream>
#include <iostream>
@ -152,6 +153,7 @@ bool loadZobov(const char *descName, const char *adjName, const char *voidsName,
for (int j = 0; j < z.allVoids[volId].zId.size(); j++)
{
int zzid = z.allVoids[volId].zId[j];
assert(zzid < z.allZones.size());
actualNumber += z.allZones[zzid].pId.size();
}

46
c_tools/libzobov/particleInfo.cpp
View file

@ -1,3 +1,4 @@
#include <cstdlib>
#include <netcdfcpp.h>
#include <CosmoTool/fortran.hpp>
#include "particleInfo.hpp"
@ -5,6 +6,34 @@
using namespace std;
using namespace CosmoTool;
template<bool failure>
double retrieve_attr_safe_double(NcFile& f, const char *name, double defval)
{
NcAtt *a = f.get_att(name);
if (a == 0)
{
if (failure)
abort();
return defval;
}
return a->as_double(0);
}
template<bool failure>
int retrieve_attr_safe_int(NcFile& f, const char *name, int defval)
{
NcAtt *a = f.get_att(name);
if (a == 0)
{
if (failure)
abort();
return defval;
}
return a->as_int(0);
}
bool loadParticleInfo(ParticleInfo& info,
const std::string& particles,
const std::string& extra_info)
@ -13,18 +42,19 @@ bool loadParticleInfo(ParticleInfo& info,
int isObservation;
NcFile f_info(extra_info.c_str());
NcError nerr(NcError::verbose_nonfatal);
if (!f_info.is_valid())
return false;
info.ranges[0][0] = f_info.get_att("range_x_min")->as_double(0);
info.ranges[0][1] = f_info.get_att("range_x_max")->as_double(0);
info.ranges[1][0] = f_info.get_att("range_y_min")->as_double(0);
info.ranges[1][1] = f_info.get_att("range_y_max")->as_double(0);
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
info.ranges[0][0] = retrieve_attr_safe_double<true>(f_info, "range_x_min", 0);
info.ranges[0][1] = retrieve_attr_safe_double<true>(f_info, "range_x_max", 0);
info.ranges[1][0] = retrieve_attr_safe_double<true>(f_info, "range_y_min", 0);
info.ranges[1][1] = retrieve_attr_safe_double<true>(f_info, "range_y_max", 0);
info.ranges[2][0] = retrieve_attr_safe_double<true>(f_info, "range_z_min", 0);
info.ranges[2][1] = retrieve_attr_safe_double<true>(f_info, "range_z_max", 0);
info.mask_index = retrieve_attr_safe_int<true>(f_info, "mask_index", 0);
isObservation = retrieve_attr_safe_int<false>(f_info, "is_observation", 0);
for (int i = 0; i < 3; i++)
info.length[i] = info.ranges[i][1] - info.ranges[i][0];

8
c_tools/mock/generateMock.cpp
View file

@ -317,9 +317,9 @@ void buildBox(SimuData *simu, long num_targets, long loaded,
for (int j = 0; j < 3; j++)
{
boxed->Pos[j][loaded] = (simu->Pos[j][pid]-ranges[j*2])*mul[j];
assert(boxed->Pos[j][loaded] > 0);
assert(boxed->Pos[j][loaded] < 1);
boxed->Pos[j][loaded] = max(min((simu->Pos[j][pid]-ranges[j*2])*mul[j], double(1)), double(0));
assert(boxed->Pos[j][loaded] >= 0);
assert(boxed->Pos[j][loaded] <= 1);
}
uniqueID[loaded] = (simu_uniqueID != 0) ? simu_uniqueID[pid] : 0;
expansion_fac[loaded] = efac[pid];
@ -400,6 +400,7 @@ void makeBoxFromParameter(SimuData *simu, SimuData* &boxed, generateMock_info& a
mul = new double[3];
ranges = new double[6];
snapshot_split = new long[*num_snapshots];
expansion_fac = new double[boxed->NumPart];
boxed->new_attribute("uniqueID", uniqueID, delete_adaptor<long>);
@ -408,6 +409,7 @@ void makeBoxFromParameter(SimuData *simu, SimuData* &boxed, generateMock_info& a
boxed->new_attribute("particle_id", particle_id, delete_adaptor<long>);
boxed->new_attribute("num_snapshots", num_snapshots, delete_adaptor<int>);
boxed->new_attribute("snapshot_split", snapshot_split, delete_adaptor<long>);
boxed->new_attribute("expansion_fac", expansion_fac, delete_adaptor<double>);
v_id->get(particle_id, boxed->NumPart);
v_snap->get(snapshot_split, *num_snapshots);

2
c_tools/mock/loaders/gadget_loader.cpp
View file

@ -77,7 +77,7 @@ public:
SimulationLoader *gadgetLoader(const std::string& snapshot, double Mpc_unitLength, int flags)
{
bool singleFile;
bool singleFile = false;
int num_files;
SimuData *d;

20
c_tools/stacking/pruneVoids.cpp
View file

@ -91,7 +91,7 @@ int main(int argc, char **argv) {
double nearestEdge, redshift;
char line[500], junkStr[10];
int mask_index;
double ranges[2][3], boxLen[3], mul;
double ranges[3][2], boxLen[3], mul;
double volNorm, radius;
int clock1, clock2;
int periodicX=0, periodicY=0, periodicZ=0;
@ -180,7 +180,7 @@ int main(int argc, char **argv) {
part[p].y += ranges[1][0];
part[p].z += ranges[2][0];
}
}
}
fclose(fp);
printf(" Read %d particles...\n", numPartTot);
@ -350,19 +350,19 @@ int main(int argc, char **argv) {
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];
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 (voids[iVoid].barycenter[1] < 0)
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];
if (voids[iVoid].barycenter[2] < 0)
voids[iVoid].barycenter[2] = boxLen[2] + voids[iVoid].barycenter[2];
}
// compute central density
@ -406,8 +406,8 @@ int main(int argc, char **argv) {
for (p = 0; p < voids[iVoid].numPart; p++) {
dist[0] = fabs(voidPart[p].x - voids[iVoid].barycenter[0]);
dist[0] = fabs(voidPart[p].y - voids[iVoid].barycenter[1]);
dist[0] = fabs(voidPart[p].z - voids[iVoid].barycenter[2]);
dist[1] = fabs(voidPart[p].y - voids[iVoid].barycenter[1]);
dist[2] = fabs(voidPart[p].z - voids[iVoid].barycenter[2]);
if (periodicX) dist[0] = fmin(dist[0], boxLen[0]-dist[0]);
if (periodicY) dist[1] = fmin(dist[1], boxLen[1]-dist[1]);
@ -599,7 +599,7 @@ int main(int argc, char **argv) {
voids[iVoid].densCon,
voids[iVoid].voidProb);
fprintf(fpBarycenter, "%d %e %e %e\n",
fprintf(fpBarycenter, "%d %e %e %e\n",
voids[iVoid].voidID,
voids[iVoid].barycenter[0],
voids[iVoid].barycenter[1],

1
external/external_python_build.cmake vendored
View file

@ -101,6 +101,7 @@ IF(INTERNAL_HEALPY)
"-DNETCDF4_DIR=${NETCDF_BIN_DIR}"
"-DPYTHON_LDFLAGS:STRING=${PYTHON_LDFLAGS}"
"-DPYTHON_LOCAL_SITE_PACKAGE=${PYTHON_LOCAL_SITE_PACKAGE}"
"-DSUPPORT_ARCH_NATIVE=${SUPPORT_ARCH_NATIVE}"
"-DTARGET_PATH=${CMAKE_BINARY_DIR}/ext_build/python" "-P")
ExternalProject_Add(healpy

3
external/python_build.cmake vendored
View file

@ -7,6 +7,9 @@ SET(ENV{PYTHONPATH} ${PYTHON_LOCAL_SITE_PACKAGE}:$ENV{PYTHONPATH})
SET(ENV{CFITSIO_EXT_INC} ${CFITSIO_EXT_INC})
SET(ENV{CFITSIO_EXT_LIB} ${CFITSIO_EXT_LIB})
SET(ENV{CFITSIO_EXT_PREFIX} ${CFITSIO_EXT_PREFIX})
IF (NOT SUPPORT_ARCH_NATIVE)
SET(ENV{HEALPY_WITHOUT_NATIVE} 1)
ENDIF(NOT SUPPORT_ARCH_NATIVE)
SET(PYTHON_BUILD_COMMAND ${PYTHON_EXECUTABLE} setup.py build)
MESSAGE(STATUS "Running ${PYTHON_BUILD_COMMAND}")

3
pipeline/generateCatalog.py
View file

@ -20,6 +20,7 @@ if (len(sys.argv) > 1):
print " Cannot find parameter file %s!" % filename
exit(-1)
parms = imp.load_source("name", filename)
regenerateFlag = False
globals().update(vars(parms))
else:
print " Using default parameters"
@ -90,7 +91,7 @@ for sample in dataSampleList:
launchGenerate(sample, GENERATE_PATH, workDir=workDir,
inputDataDir=inputDataDir, zobovDir=zobovDir,
figDir=figDir, logFile=logFile, useLCDM=useLCDM,
continueRun=continueRun)
continueRun=continueRun, regenerate=regenerateFlag)
# --------------------------------------------------------------------------
if (startCatalogStage <= 2) and (endCatalogStage >= 2) and not sample.isCombo:

1
python_tools/pipeline_source/prepareCatalogs.in.py
View file

@ -81,6 +81,7 @@ endCatalogStage = 4
startAPStage = 1
endAPStage = 1
regenerateFlag = False
ZOBOV_PATH = "@CMAKE_BINARY_DIR@/zobov/"
CTOOLS_PATH = "@CMAKE_BINARY_DIR@/c_tools/"
freshStack = True

44
python_tools/void_python_tools/backend/launchers.py
View file

@ -24,11 +24,18 @@ ncFloat = 'f8' # Double precision
# -----------------------------------------------------------------------------
def launchGenerate(sample, binPath, workDir=None, inputDataDir=None,
zobovDir=None, figDir=None, logFile=None, useLCDM=False,
continueRun=None):
continueRun=None,regenerate=False):
if sample.dataType == "observation":
sampleName = sample.fullName
if regenerate:
inputParameterFlag = "inputParameter " + zobovDir+"/zobov_slice_"+sampleName+".par"
outputFile = zobovDir+"/regenerated_zobov_slice_" + sampleName
else:
inputParameterFlag = ""
outputFile = zobovDir+"/zobov_slice_" + sampleName
if sample.dataFile == "":
datafile = inputDataDir+"/"+sampleName
else:
@ -50,16 +57,17 @@ def launchGenerate(sample, binPath, workDir=None, inputDataDir=None,
zMax %g
density_fake %g
%s
""" % (datafile, maskFile, zobovDir+"/zobov_slice_"+sampleName,
%s
""" % (datafile, maskFile, outputFile,
zobovDir+"/zobov_slice_"+sampleName+".par",
sample.zBoundary[0], sample.zBoundary[1], sample.fakeDensity,
useLCDMFlag)
useLCDMFlag, inputParameterFlag)
parmFile = os.getcwd()+"/generate_"+sample.fullName+".par"
file(parmFile, mode="w").write(conf)
if not (continueRun and jobSuccessful(logFile, "Done!\n")):
if regenerate or not (continueRun and jobSuccessful(logFile, "Done!\n")):
cmd = "%s --configFile=%s &> %s" % (binPath,parmFile,logFile)
os.system(cmd)
if jobSuccessful(logFile, "Done!\n"):
@ -97,6 +105,13 @@ def launchGenerate(sample, binPath, workDir=None, inputDataDir=None,
datafile = inputDataDir+"/"+sample.dataFile
if regenerate:
inputParameterFlag = "inputParameter " + zobovDir+"/zobov_slice_"+sampleName+".par"
outputFile = zobovDir+"/regenerated_zobov_slice_" + sampleName
else:
inputParameterFlag = ""
outputFile = zobovDir+"/zobov_slice_" + sampleName
if sample.usePecVel:
includePecVelString = "peculiarVelocities"
else:
@ -134,20 +149,21 @@ def launchGenerate(sample, binPath, workDir=None, inputDataDir=None,
rangeZ_min %g
rangeZ_max %g
subsample %g
""" % (dataFileLine, zobovDir+"/zobov_slice_"+sampleName,
%s
""" % (dataFileLine, outputFile,
zobovDir+"/zobov_slice_"+sampleName+".par",
includePecVelString,
useLightConeString,
sample.dataUnit,
xMin, xMax, yMin, yMax,
sample.zBoundaryMpc[0], sample.zBoundaryMpc[1],
sample.subsample)
sample.subsample,inputParameterFlag)
parmFile = os.getcwd()+"/generate_"+sample.fullName+".par"
file(parmFile, mode="w").write(conf)
if not (continueRun and jobSuccessful(logFile, "Done!\n")):
if regenerate or not (continueRun and jobSuccessful(logFile, "Done!\n")):
cmd = "%s --configFile=%s &> %s" % (binPath,parmFile,logFile)
os.system(cmd)
if jobSuccessful(logFile, "Done!\n"):
@ -258,6 +274,7 @@ def launchPrune(sample, binPath, thisDataPortion=None,
sample.boxLen <= 1.e-1:
periodicLine += "z"
periodicLine += "' "
periodicLine = ""
if not (continueRun and jobSuccessful(logFile, "NetCDF: Not a valid ID\n")):
cmd = binPath
@ -300,6 +317,9 @@ def launchPrune(sample, binPath, thisDataPortion=None,
str(thisDataPortion)+"_"+\
str(sampleName)+".out"
cmd += " &> " + logFile
f=file("run_prune.sh",mode="w")
f.write(cmd)
f.close()
os.system(cmd)
if jobSuccessful(logFile, "NetCDF: Not a valid ID\n") or \
@ -383,14 +403,14 @@ def launchStack(sample, stack, binPath, thisDataPortion=None, logDir=None,
voidDir=None, freshStack=True, runSuffix=None,
zobovDir=None,
INCOHERENT=False, ranSeed=None, summaryFile=None,
continueRun=None, dataType=None):
continueRun=None, dataType=None, prefixRun=""):
sampleName = sample.fullName
runSuffix = getStackSuffix(stack.zMin, stack.zMax, stack.rMin,
stack.rMax, thisDataPortion)
logFile = logDir+"/stack_"+sampleName+"_"+runSuffix+".out"
logFile = logDir+("/%sstack_"%prefixRun)+sampleName+"_"+runSuffix+".out"
treeFile = voidDir+"/tree.data"
@ -417,7 +437,7 @@ def launchStack(sample, stack, binPath, thisDataPortion=None, logDir=None,
maxDen = 0.2*float(maskIndex)/float(totalPart)
else:
maskIndex = 999999999
maxDen = 0.2
maxDen = -0.8
if INCOHERENT:
nullTestFlag = "INCOHERENT"
@ -458,7 +478,7 @@ def launchStack(sample, stack, binPath, thisDataPortion=None, logDir=None,
zobovDir+"/vol_"+sampleName+".dat",
stack.rMin,
stack.rMax,
zobovDir+"/zobov_slice_"+sampleName,
zobovDir+("/%szobov_slice_"%prefixRun)+sampleName,
zobovDir+"/zobov_slice_"+sampleName+".par",
maxDen,
centralRadius,
@ -474,7 +494,7 @@ def launchStack(sample, stack, binPath, thisDataPortion=None, logDir=None,
zobovDir+"/boundaryDistances_"+thisDataPortion+"_"+sampleName+".out",
rescaleFlag)
parmFile = os.getcwd()+"/stack_"+sample.fullName+".par"
parmFile = os.getcwd()+("/%sstack_"%prefixRun)+sample.fullName+".par"
fp = file(parmFile, mode="w")
fp.write(conf)

33
zobov/voztie.c
View file

@ -8,6 +8,7 @@ int main(int argc, char *argv[]) {
FILE *part, *adj, *vol;
char partfile[200], *suffix, adjfile[200], volfile[200], *outDir;
float *vols, volstemp;
int *cnt_adj;
PARTADJ *adjs;
@ -78,13 +79,17 @@ int main(int argc, char *argv[]) {
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");
adjs = (PARTADJ *)malloc(np*sizeof(PARTADJ));
if (adjs == NULL) printf("Couldn't allocate adjs.\n");
vols = (float *)malloc(np*sizeof(float));
if (vols == NULL) printf("Couldn't allocate vols.\n");
orig = (int *)malloc(nvpmax*sizeof(int));
if (orig == NULL) printf("Couldn't allocate orig.\n");
if ((vols == NULL) || (orig == NULL) || (adjs == NULL)) {
if ((cnt_adj==NULL) || (vols == NULL) || (orig == NULL) || (adjs == NULL)) {
printf("Not enough memory to allocate. Exiting.\n");
exit(0);
}
@ -238,11 +243,24 @@ printf("\n");
// END OMS
/* 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++)
cnt_adj[i] = 0;
for(i=0;i<mockIndex;i++)
{
for (j=0;j<adjs[i].nadj;j++)
{
cnt_adj[adjs[i].adj[j]]++;
cnt_adj[i]++;
}
}
// PMS
for (i=0;i<mockIndex;i++)
//for (i=0;i<np;i++)
// END PMS
fwrite(&adjs[i].nadj,1,sizeof(int),adj);
fwrite(&cnt_adj[i],1,sizeof(int),adj);
/* Now the lists of adjacencies (without double counting) */
// PMS
@ -253,9 +271,11 @@ printf("\n");
nout = 0;
for (j=0;j<adjs[i].nadj; j++) if (adjs[i].adj[j] > i) nout++;
fwrite(&nout,1,sizeof(int),adj);
for (j=0;j<adjs[i].nadj; j++)
if (adjs[i].adj[j] > i)
for (j=0;j<adjs[i].nadj; j++) {
int id = adjs[i].adj[j];
if (id > i)
fwrite(&(adjs[i].adj[j]),1,sizeof(int),adj);
}
}
fclose(adj);
@ -275,5 +295,10 @@ printf("\n");
fclose(vol);
free(vols);
free(cnt_adj);
free(adjs);
free(orig);
return(0);
}