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Merged in python3 (pull request #5)

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Port to python3, large code cleanup

* Fixed command line for cosmotool

* Fix path

* Dump command line is log file

* Fix important typo

* Modify paths for example

* Fix path again

* Use an explicit constructor

* Change file to open (python 2->3)

* python3 fix for xrange in periodic_kdtree.py

* Fixed index for Np, numPart, numZones, numZonesTot, partID, zoneID in catalogUtil.py
This commit is contained in:
Guilhem Lavaux 2020-12-29 08:56:33 +00:00
parent 8249256508
commit affb56ff48
392 changed files with 4092 additions and 260938 deletions
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5
c_tools/libzobov/CMakeLists.txt
View file

@ -2,7 +2,4 @@
add_library(zobovTool loadZobov.cpp particleInfo.cpp contour_pixels.cpp)
set_target_properties(zobovTool PROPERTIES COMPILE_FLAGS ${OpenMP_CXX_FLAGS} LINK_FLAGS ${OpenMP_CXX_FLAGS})
SET(ZOB_LIBS zobovTool ${COSMOTOOL_LIBRARY} ${GSL_LIBRARY} ${GSLCBLAS_LIBRARY} ${NETCDFCPP_LIBRARY} ${NETCDF_LIBRARY})
SET(ZOB_LIBS PARENT ${ZOB_LIBS})
target_link_libraries(zobovTool ${COSMOTOOL_LIBRARY} ${GSL_LIBRARIES} ${NETCDF_LIBRARIES} ${HDF5_CXX_LIBRARIES} ${HDF5_HL_LIBRARIES} ${HDF5_LIBRARIES} ${DL_LIBRARY})

141
c_tools/libzobov/particleInfo.cpp
View file

@ -17,118 +17,121 @@
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+*/
#include <cstdlib>
#include <netcdfcpp.h>
#include <CosmoTool/fortran.hpp>
#include "particleInfo.hpp"
#include <CosmoTool/fortran.hpp>
#include <cstdlib>
#include <netcdf>
using namespace std;
using namespace CosmoTool;
using namespace netCDF;
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>
double retrieve_attr_safe_double(NcFile& f, const char* name, double defval) {
NcGroupAtt a = f.getAtt(name);
if (a.isNull()) {
if (failure) abort();
return defval;
}
if (a.getAttLength() != 1) {
abort();
}
double x;
a.getValues(&x);
return x;
}
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);
template <bool failure>
int retrieve_attr_safe_int(NcFile& f, const char* name, int defval) {
NcGroupAtt a = f.getAtt(name);
if (a.isNull()) {
if (failure) abort();
return defval;
}
if (a.getAttLength() != 1) {
abort();
}
int x;
a.getValues(&x);
return x;
}
bool loadParticleInfo(ParticleInfo& info, const std::string& particles,
const std::string& extra_info) {
int numpart;
int isObservation;
bool loadParticleInfo(ParticleInfo& info,
const std::string& particles,
const std::string& extra_info)
{
int numpart;
int isObservation;
try {
NcFile f_info(extra_info, NcFile::read);
NcFile f_info(extra_info.c_str());
NcError nerr(NcError::verbose_nonfatal);
if (!f_info.is_valid())
return false;
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);
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];
for (int i = 0; i < 3; i++)
info.length[i] = info.ranges[i][1] - info.ranges[i][0];
try
{
try {
UnformattedRead f(particles);
float mul, offset;
f.beginCheckpoint();
numpart = f.readInt32();
f.endCheckpoint();
info.particles.resize(numpart);
offset = info.ranges[0][0];
// TEST PMS NON-COBIC BOXES
//mul = 1.0;
// mul = 1.0;
mul = info.ranges[0][1] - info.ranges[0][0];
f.beginCheckpoint();
for (int i = 0; i < numpart; i++)
info.particles[i].x = mul*f.readReal32();
info.particles[i].x = mul * f.readReal32();
f.endCheckpoint();
offset = info.ranges[1][0];
//mul = 1.0;
// mul = 1.0;
mul = info.ranges[1][1] - info.ranges[1][0];
f.beginCheckpoint();
for (int i = 0; i < numpart; i++)
info.particles[i].y = mul*f.readReal32();
info.particles[i].y = mul * f.readReal32();
f.endCheckpoint();
offset = info.ranges[2][0];
//mul = 1.0;
// mul = 1.0;
mul = info.ranges[2][1] - info.ranges[2][0];
f.beginCheckpoint();
for (int i = 0; i < numpart; i++)
info.particles[i].z = mul*f.readReal32();
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];
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)
{
} catch (NoSuchFileException const& e) {
return false;
}
} catch (exceptions::NcCantRead const&) {
return false;
}
return true;
}