mirror of
https://bitbucket.org/cosmicvoids/vide_public.git
synced 2025-07-04 07:11:12 +00:00
Merged in python3 (pull request #5)
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:
parent
8249256508
commit
affb56ff48
392 changed files with 4092 additions and 260938 deletions
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@ -30,10 +30,6 @@ ELSE (CAIROMMCONFIG_INCLUDE_PATH AND CAIROMM_INCLUDE_PATH AND SIGC_INCLUDE_PATH
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ENDIF (CAIROMMCONFIG_INCLUDE_PATH AND CAIROMM_INCLUDE_PATH AND SIGC_INCLUDE_PATH AND SIGCCONFIG_INCLUDE_PATH AND CAIRO_INCLUDE_PATH AND FREETYPE_INCLUDE_PATH AND CAIROMM_LIB)
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SET(ZOB_LIBS zobovTool
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${COSMOTOOL_LIBRARY} ${GSL_LIBRARIES}
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${NETCDF_LIBRARIES} ${DL_LIB})
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include_directories(
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${QHULL_INCLUDES}
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@ -41,6 +37,8 @@ include_directories(
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${CMAKE_CURRENT_BINARY_DIR}
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${CMAKE_CURRENT_SOURCE_DIR}/libzobov)
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SET(ZOB_LIBS zobovTool)
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set(computeAverageDistortion_SRCS computeAverageDistortion.cpp)
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add_genopt(computeAverageDistortion_SRCS computeAverageDistortion.ggo computeAverageDistortion_conf STRUCTNAME Params)
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@ -4,3 +4,5 @@ SET(voidOverlap_SRCS voidOverlap.cpp)
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add_genopt(voidOverlap_SRCS voidOverlap.ggo voidOverlap_conf STRUCTNAME voidOverlap_info)
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add_executable(voidOverlap ${voidOverlap_SRCS})
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target_link_libraries(voidOverlap ${ZOB_LIBS})
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install(TARGETS voidOverlap DESTINATION ${VIDE_BIN})
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@ -36,7 +36,7 @@
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#include <math.h>
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#include "voidOverlap_conf.h"
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#include <vector>
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#include <netcdfcpp.h>
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#include <netcdf>
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#include <iostream>
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#include <sstream>
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#include <fstream>
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@ -546,13 +546,13 @@ void loadCatalog(const char *partFile, const char *volFile,
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float ranges[3][2];
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printf("Loading info...\n");
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NcFile f_info(infoFile);
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ranges[0][0] = f_info.get_att("range_x_min")->as_double(0);
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ranges[0][1] = f_info.get_att("range_x_max")->as_double(0);
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ranges[1][0] = f_info.get_att("range_y_min")->as_double(0);
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ranges[1][1] = f_info.get_att("range_y_max")->as_double(0);
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ranges[2][0] = f_info.get_att("range_z_min")->as_double(0);
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ranges[2][1] = f_info.get_att("range_z_max")->as_double(0);
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netCDF::NcFile f_info(infoFile, netCDF::NcFile::read);
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f_info.getAtt("range_x_min").getValues(&ranges[0][0]);
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f_info.getAtt("range_x_max").getValues(&ranges[0][1]);
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f_info.getAtt("range_y_min").getValues(&ranges[1][0]);
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f_info.getAtt("range_y_max").getValues(&ranges[1][1]);
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f_info.getAtt("range_z_min").getValues(&ranges[2][0]);
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f_info.getAtt("range_z_max").getValues(&ranges[2][1]);
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catalog.boxLen[0] = ranges[0][1] - ranges[0][0];
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catalog.boxLen[1] = ranges[1][1] - ranges[1][0];
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@ -26,3 +26,4 @@ SET(hod_SRCS header.c main.c utility.c sigmac.c
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)
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add_executable(hod ${hod_SRCS})
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target_link_libraries(hod -lm)
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install(TARGETS hod DESTINATION ${VIDE_BIN})
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@ -94,3 +94,4 @@ struct perform_tasks Task;
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struct workspace Work;
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struct COLOR_DATA wp_color;
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struct m2n_workspace M2N;
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struct WP wp;
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@ -371,7 +371,7 @@ extern struct hod_parameters {
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/* Structure to keep information/data about fitting
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* color-defined samples.
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*/
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struct COLOR_DATA {
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extern struct COLOR_DATA {
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int ON;
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double ngal_red;
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double ngal_blue;
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@ -383,8 +383,7 @@ struct COLOR_DATA {
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double *e_red,*e_blue,*e_full;
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double *x_red,*x_blue,*x_full;
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double **covar_red, **covar_blue, **covar_full;
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} wp_color;
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};
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/* This is to put the work done in xi_multipoles into
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* a global space.
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@ -530,7 +529,7 @@ extern struct perform_tasks {
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/* Workspace for w_p minimzation.
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*/
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struct WP {
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extern struct WP {
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double **covar;
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int np;
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int ncf;
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@ -2,7 +2,4 @@
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add_library(zobovTool loadZobov.cpp particleInfo.cpp contour_pixels.cpp)
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set_target_properties(zobovTool PROPERTIES COMPILE_FLAGS ${OpenMP_CXX_FLAGS} LINK_FLAGS ${OpenMP_CXX_FLAGS})
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SET(ZOB_LIBS zobovTool ${COSMOTOOL_LIBRARY} ${GSL_LIBRARY} ${GSLCBLAS_LIBRARY} ${NETCDFCPP_LIBRARY} ${NETCDF_LIBRARY})
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SET(ZOB_LIBS PARENT ${ZOB_LIBS})
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target_link_libraries(zobovTool ${COSMOTOOL_LIBRARY} ${GSL_LIBRARIES} ${NETCDF_LIBRARIES} ${HDF5_CXX_LIBRARIES} ${HDF5_HL_LIBRARIES} ${HDF5_LIBRARIES} ${DL_LIBRARY})
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@ -17,118 +17,121 @@
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51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
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+*/
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#include <cstdlib>
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#include <netcdfcpp.h>
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#include <CosmoTool/fortran.hpp>
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#include "particleInfo.hpp"
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#include <CosmoTool/fortran.hpp>
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#include <cstdlib>
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#include <netcdf>
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using namespace std;
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using namespace CosmoTool;
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using namespace netCDF;
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template<bool failure>
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double retrieve_attr_safe_double(NcFile& f, const char *name, double defval)
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{
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NcAtt *a = f.get_att(name);
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if (a == 0)
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{
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if (failure)
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abort();
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return defval;
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}
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return a->as_double(0);
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template <bool failure>
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double retrieve_attr_safe_double(NcFile& f, const char* name, double defval) {
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NcGroupAtt a = f.getAtt(name);
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if (a.isNull()) {
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if (failure) abort();
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return defval;
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}
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if (a.getAttLength() != 1) {
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abort();
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}
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double x;
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a.getValues(&x);
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return x;
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}
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template<bool failure>
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int retrieve_attr_safe_int(NcFile& f, const char *name, int defval)
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{
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NcAtt *a = f.get_att(name);
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if (a == 0)
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{
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if (failure)
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abort();
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return defval;
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}
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return a->as_int(0);
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template <bool failure>
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int retrieve_attr_safe_int(NcFile& f, const char* name, int defval) {
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NcGroupAtt a = f.getAtt(name);
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if (a.isNull()) {
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if (failure) abort();
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return defval;
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}
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if (a.getAttLength() != 1) {
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abort();
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}
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int x;
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a.getValues(&x);
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return x;
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}
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bool loadParticleInfo(ParticleInfo& info, const std::string& particles,
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const std::string& extra_info) {
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int numpart;
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int isObservation;
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bool loadParticleInfo(ParticleInfo& info,
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const std::string& particles,
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const std::string& extra_info)
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{
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int numpart;
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int isObservation;
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try {
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NcFile f_info(extra_info, NcFile::read);
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NcFile f_info(extra_info.c_str());
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NcError nerr(NcError::verbose_nonfatal);
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if (!f_info.is_valid())
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return false;
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info.ranges[0][0] =
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retrieve_attr_safe_double<true>(f_info, "range_x_min", 0);
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info.ranges[0][1] =
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retrieve_attr_safe_double<true>(f_info, "range_x_max", 0);
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info.ranges[1][0] =
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retrieve_attr_safe_double<true>(f_info, "range_y_min", 0);
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info.ranges[1][1] =
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retrieve_attr_safe_double<true>(f_info, "range_y_max", 0);
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info.ranges[2][0] =
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retrieve_attr_safe_double<true>(f_info, "range_z_min", 0);
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info.ranges[2][1] =
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retrieve_attr_safe_double<true>(f_info, "range_z_max", 0);
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info.mask_index = retrieve_attr_safe_int<true>(f_info, "mask_index", 0);
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isObservation = retrieve_attr_safe_int<false>(f_info, "is_observation", 0);
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info.ranges[0][0] = retrieve_attr_safe_double<true>(f_info, "range_x_min", 0);
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info.ranges[0][1] = retrieve_attr_safe_double<true>(f_info, "range_x_max", 0);
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info.ranges[1][0] = retrieve_attr_safe_double<true>(f_info, "range_y_min", 0);
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info.ranges[1][1] = retrieve_attr_safe_double<true>(f_info, "range_y_max", 0);
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info.ranges[2][0] = retrieve_attr_safe_double<true>(f_info, "range_z_min", 0);
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info.ranges[2][1] = retrieve_attr_safe_double<true>(f_info, "range_z_max", 0);
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info.mask_index = retrieve_attr_safe_int<true>(f_info, "mask_index", 0);
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isObservation = retrieve_attr_safe_int<false>(f_info, "is_observation", 0);
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for (int i = 0; i < 3; i++)
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info.length[i] = info.ranges[i][1] - info.ranges[i][0];
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for (int i = 0; i < 3; i++)
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info.length[i] = info.ranges[i][1] - info.ranges[i][0];
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try
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{
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try {
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UnformattedRead f(particles);
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float mul, offset;
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f.beginCheckpoint();
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numpart = f.readInt32();
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f.endCheckpoint();
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info.particles.resize(numpart);
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offset = info.ranges[0][0];
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// TEST PMS NON-COBIC BOXES
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//mul = 1.0;
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// mul = 1.0;
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mul = info.ranges[0][1] - info.ranges[0][0];
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f.beginCheckpoint();
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for (int i = 0; i < numpart; i++)
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info.particles[i].x = mul*f.readReal32();
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info.particles[i].x = mul * f.readReal32();
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f.endCheckpoint();
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offset = info.ranges[1][0];
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//mul = 1.0;
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// mul = 1.0;
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mul = info.ranges[1][1] - info.ranges[1][0];
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f.beginCheckpoint();
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for (int i = 0; i < numpart; i++)
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info.particles[i].y = mul*f.readReal32();
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info.particles[i].y = mul * f.readReal32();
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f.endCheckpoint();
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offset = info.ranges[2][0];
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//mul = 1.0;
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// mul = 1.0;
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mul = info.ranges[2][1] - info.ranges[2][0];
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f.beginCheckpoint();
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for (int i = 0; i < numpart; i++)
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info.particles[i].z = mul*f.readReal32();
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info.particles[i].z = mul * f.readReal32();
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f.endCheckpoint();
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if (!isObservation) {
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for (int i = 0; i < numpart; i++) {
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info.particles[i].x += info.ranges[0][0];
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info.particles[i].y += info.ranges[1][0];
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info.particles[i].z += info.ranges[2][0];
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info.particles[i].x += info.ranges[0][0];
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info.particles[i].y += info.ranges[1][0];
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info.particles[i].z += info.ranges[2][0];
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}
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}
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}
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catch (const NoSuchFileException& e)
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{
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} catch (NoSuchFileException const& e) {
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return false;
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}
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} catch (exceptions::NcCantRead const&) {
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return false;
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}
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return true;
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}
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@ -7,7 +7,7 @@ ENDIF(SDF_SUPPORT)
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SET(generateMock_SRCS generateMock.cpp )
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add_genopt(generateMock_SRCS generateMock.ggo generateMock_conf STRUCTNAME generateMock_info)
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add_executable(generateMock ${generateMock_SRCS})
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target_link_libraries(generateMock simu_loaders ${ZOB_LIBS} ${HDF5HL_CPP_LIBRARY} ${HDF5_CPP_LIBRARY} ${HDF5_LIBRARY} ${LIBSDF_LIBRARY})
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target_link_libraries(generateMock simu_loaders ${ZOB_LIBS} ${LIBSDF_LIBRARY} ${HDF5_CXX_LIBRARIES} ${HDF5_HL_LIBRARIES} ${HDF5_LIBRARIES} ${DL_LIBRARY})
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add_executable(generateTestMock generateTestMock.cpp)
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target_link_libraries(generateTestMock ${ZOB_LIBS})
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@ -16,8 +16,11 @@ target_link_libraries(generateTestMock ${ZOB_LIBS})
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SET(generateFromCatalog_SRCS generateFromCatalog.cpp)
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add_genopt(generateFromCatalog_SRCS generateFromCatalog.ggo generateFromCatalog_conf STRUCTNAME generateFromCatalog_info)
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add_executable(generateFromCatalog ${generateFromCatalog_SRCS})
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target_link_libraries(generateFromCatalog ${ZOB_LIBS} ${HDF5HL_CPP_LIBRARY} ${HDF5_CPP_LIBRARY} ${HEALPIX_LIBRARIES})
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target_link_libraries(generateFromCatalog ${ZOB_LIBS} ${HDF5_CXX_LIBRARIES} ${HDF5_HL_LIBRARIES} ${HDF5_LIBRARIES} ${HEALPIX_LIBRARIES} ${DL_LIBRARY})
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set_target_properties(generateFromCatalog PROPERTIES COMPILE_FLAGS ${OpenMP_CXX_FLAGS} LINK_FLAGS ${OpenMP_CXX_FLAGS})
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subdirs(loaders)
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install(TARGETS generateMock generateTestMock generateFromCatalog DESTINATION ${VIDE_BIN})
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@ -28,7 +28,7 @@
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#include <string>
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#include "generateFromCatalog_conf.h"
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#include "contour_pixels.hpp"
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#include <netcdfcpp.h>
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#include <netcdf>
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#include <CosmoTool/fortran.hpp>
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#include <gsl/gsl_interp.h>
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#include <gsl/gsl_integration.h>
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@ -38,6 +38,7 @@
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using namespace std;
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using boost::format;
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using namespace CosmoTool;
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using namespace netCDF;
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struct NYU_Data
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{
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@ -457,13 +458,11 @@ void generateSurfaceMask(generateFromCatalog_info& args ,
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void saveData(ParticleData& pdata)
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{
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NcFile f("particles.nc", NcFile::Replace);
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assert(f.is_valid());
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NcFile f("particles.nc", NcFile::replace);
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NcDim *d = f.add_dim("space", 3);
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NcDim *p = f.add_dim("Np", pdata.pos.size());
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NcVar *v = f.add_var("particles", ncDouble, d, p);
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NcDim d = f.addDim("space", 3);
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NcDim p = f.addDim("Np", pdata.pos.size());
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NcVar v = f.addVar("particles", ncDouble, {d, p});
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double *x = new double[pdata.pos.size()];
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for (int j = 0; j < 3; j++)
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@ -472,11 +471,11 @@ void saveData(ParticleData& pdata)
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for (int i = 0; i < pdata.pos.size(); i++)
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x[i] = pdata.pos[i].xyz[j];
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v->put_rec(d, x, j);
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v.putVar({size_t(j), 0}, {1, pdata.pos.size()}, x);
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}
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v = f.add_var("id_gal", ncInt, p);
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v->put(&pdata.id_gal[0], pdata.id_gal.size());
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v = f.addVar("id_gal", ncInt, std::vector<NcDim>({p}));
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v.putVar(&pdata.id_gal[0]);
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delete[] x;
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@ -533,30 +532,30 @@ void saveForZobov(ParticleData& pdata, const string& fname, const string& paramn
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}
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f.endCheckpoint();
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NcFile fp(paramname.c_str(), NcFile::Replace);
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NcFile fp(paramname.c_str(), NcFile::replace);
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fp.add_att("range_x_min", -Lmax/100.);
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fp.add_att("range_x_max", Lmax/100.);
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fp.add_att("range_y_min", -Lmax/100.);
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fp.add_att("range_y_max", Lmax/100.);
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fp.add_att("range_z_min", -Lmax/100.);
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fp.add_att("range_z_max", Lmax/100.);
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fp.add_att("mask_index", pdata.mask_index); // PMS
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fp.add_att("is_observation", 1); // PMS
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fp.putAtt("range_x_min", ncDouble, -Lmax/100.);
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fp.putAtt("range_x_max", ncDouble, Lmax/100.);
|
||||
fp.putAtt("range_y_min", ncDouble, -Lmax/100.);
|
||||
fp.putAtt("range_y_max", ncDouble, Lmax/100.);
|
||||
fp.putAtt("range_z_min", ncDouble, -Lmax/100.);
|
||||
fp.putAtt("range_z_max", ncDouble, Lmax/100.);
|
||||
fp.putAtt("mask_index", ncInt, pdata.mask_index); // PMS
|
||||
fp.putAtt("is_observation", ncInt, 1); // PMS
|
||||
|
||||
int nOutputPart = pdata.mask_index;
|
||||
//int nOutputPart = pdata.pos.size();
|
||||
|
||||
NcDim *NumPart_dim = fp.add_dim("numpart_dim", nOutputPart);
|
||||
NcVar *v = fp.add_var("particle_ids", ncInt, NumPart_dim);
|
||||
//NcVar *v2 = fp.add_var("expansion", ncDouble, NumPart_dim);
|
||||
NcDim NumPart_dim = fp.addDim("numpart_dim", nOutputPart);
|
||||
NcVar v = fp.addVar("particle_ids", ncInt, NumPart_dim);
|
||||
//NcVar v2 = fp.addVar("expansion", ncDouble, NumPart_dim);
|
||||
|
||||
//double *expansion_fac = new double[pdata.pos.size()];
|
||||
|
||||
//for (int i = 0; i < pdata.pos.size(); i++)
|
||||
// expansion_fac[i] = 1.0;
|
||||
|
||||
v->put(&pdata.id_gal[0], nOutputPart);
|
||||
v.putVar({0}, {size_t(nOutputPart)}, &pdata.id_gal[0]);
|
||||
//v2->put(expansion_fac, pdata.pos.size());
|
||||
|
||||
//delete[] expansion_fac;
|
||||
|
|
|
|||
|
|
@ -36,12 +36,13 @@
|
|||
#include <CosmoTool/algo.hpp>
|
||||
#include "generateMock_conf.h"
|
||||
#include "gslIntegrate.hpp"
|
||||
#include <netcdfcpp.h>
|
||||
#include <netcdf>
|
||||
#include "simulation_loader.hpp"
|
||||
|
||||
using namespace std;
|
||||
using namespace CosmoTool;
|
||||
using boost::format;
|
||||
using namespace netCDF;
|
||||
|
||||
#define LIGHT_SPEED 299792.458
|
||||
|
||||
|
|
@ -426,7 +427,7 @@ void buildBox(SimuData *simu, long num_targets, long loaded,
|
|||
void saveBox(SimuData *&boxed, const std::string& outbox, generateMock_info& args_info)
|
||||
{
|
||||
double *ranges = boxed->as<double>("ranges");
|
||||
NcFile f(outbox.c_str(), NcFile::Replace, 0, 0, NcFile::Netcdf4);
|
||||
NcFile f(outbox.c_str(), NcFile::replace);
|
||||
long *particle_id = boxed->as<long>("particle_id");
|
||||
double *expansion_fac = boxed->as<double>("expansion_fac");
|
||||
long *snapshot_split = boxed->as<long>("snapshot_split");
|
||||
|
|
@ -436,56 +437,51 @@ void saveBox(SimuData *&boxed, const std::string& outbox, generateMock_info& arg
|
|||
float *velY = boxed->Vel[1];
|
||||
float *velZ = boxed->Vel[2];
|
||||
|
||||
if (!f.is_valid())
|
||||
{
|
||||
cerr << "Could not create parameter file '" << outbox << "'. Aborting." << endl;
|
||||
exit(1);
|
||||
}
|
||||
f.add_att("range_x_min", ranges[0]);
|
||||
f.add_att("range_x_max", ranges[1]);
|
||||
f.add_att("range_y_min", ranges[2]);
|
||||
f.add_att("range_y_max", ranges[3]);
|
||||
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);
|
||||
f.add_att("data_subsampling", args_info.subsample_arg);
|
||||
f.putAtt("range_x_min", ncDouble, ranges[0]);
|
||||
f.putAtt("range_x_max", ncDouble, ranges[1]);
|
||||
f.putAtt("range_y_min", ncDouble, ranges[2]);
|
||||
f.putAtt("range_y_max", ncDouble, ranges[3]);
|
||||
f.putAtt("range_z_min", ncDouble, ranges[4]);
|
||||
f.putAtt("range_z_max", ncDouble, ranges[5]);
|
||||
f.putAtt("mask_index", ncInt, -1);
|
||||
f.putAtt("is_observation", ncInt, 0);
|
||||
f.putAtt("data_subsampling", ncInt, args_info.subsample_arg);
|
||||
|
||||
NcDim *NumPart_dim = f.add_dim("numpart_dim", boxed->NumPart);
|
||||
NcDim *NumSnap_dim = f.add_dim("numsnap_dim", num_snapshots);
|
||||
NcVar *v = f.add_var("particle_ids", ncLong, NumPart_dim);
|
||||
NcVar *v2 = f.add_var("expansion", ncDouble, NumPart_dim);
|
||||
NcVar *v3 = f.add_var("snapshot_split", ncLong, NumSnap_dim);
|
||||
NcDim NumPart_dim = f.addDim("numpart_dim", boxed->NumPart);
|
||||
NcDim NumSnap_dim = f.addDim("numsnap_dim", num_snapshots);
|
||||
NcVar v = f.addVar("particle_ids", ncInt64, NumPart_dim);
|
||||
NcVar v2 = f.addVar("expansion", ncDouble, NumPart_dim);
|
||||
NcVar v3 = f.addVar("snapshot_split", ncInt64, NumSnap_dim);
|
||||
|
||||
v->put(particle_id, boxed->NumPart);
|
||||
v2->put(expansion_fac, boxed->NumPart);
|
||||
v3->put(snapshot_split, num_snapshots);
|
||||
v.putVar({0}, {size_t(boxed->NumPart)}, particle_id);
|
||||
v2.putVar({0}, {size_t(boxed->NumPart)}, expansion_fac);
|
||||
v3.putVar({0}, {size_t(boxed->NumPart)}, snapshot_split);
|
||||
if (uniqueID != 0)
|
||||
{
|
||||
NcVar *v4 = f.add_var("unique_ids_lsb", ncLong, NumPart_dim);
|
||||
NcVar *v5 = f.add_var("unique_ids_msb", ncLong, NumPart_dim);
|
||||
NcVar v4 = f.addVar("unique_ids_lsb", ncInt, NumPart_dim);
|
||||
NcVar v5 = f.addVar("unique_ids_msb", ncInt, NumPart_dim);
|
||||
|
||||
nclong *tmp_int = new nclong[boxed->NumPart];
|
||||
for (long i = 0; i < boxed->NumPart; i++)
|
||||
tmp_int[i] = (nclong)(((unsigned long)uniqueID[i]) & 0xffffffff);
|
||||
v4->put(tmp_int, boxed->NumPart);
|
||||
v4.putVar({0}, {size_t(boxed->NumPart)}, tmp_int);
|
||||
for (long i = 0; i < boxed->NumPart; i++)
|
||||
tmp_int[i] = (nclong)((((unsigned long)uniqueID[i]) & 0xffffffff) >> 32);
|
||||
v5->put(tmp_int, boxed->NumPart);
|
||||
v5.putVar({0}, {size_t(boxed->NumPart)}, tmp_int);
|
||||
delete[] tmp_int;
|
||||
}
|
||||
|
||||
NcVar *v6 = f.add_var("vel_x", ncFloat, NumPart_dim);
|
||||
NcVar *v7 = f.add_var("vel_y", ncFloat, NumPart_dim);
|
||||
NcVar *v8 = f.add_var("vel_z", ncFloat, NumPart_dim);
|
||||
v6->put(velX, boxed->NumPart);
|
||||
v7->put(velY, boxed->NumPart);
|
||||
v8->put(velZ, boxed->NumPart);
|
||||
NcVar v6 = f.addVar("vel_x", ncFloat, NumPart_dim);
|
||||
NcVar v7 = f.addVar("vel_y", ncFloat, NumPart_dim);
|
||||
NcVar v8 = f.addVar("vel_z", ncFloat, NumPart_dim);
|
||||
v6.putVar({0}, {size_t(boxed->NumPart)}, velX);
|
||||
v7.putVar({0}, {size_t(boxed->NumPart)}, velY);
|
||||
v8.putVar({0}, {size_t(boxed->NumPart)}, velZ);
|
||||
}
|
||||
|
||||
void makeBoxFromParameter(SimuData *simu, SimuData* &boxed, generateMock_info& args_info)
|
||||
{
|
||||
NcFile f(args_info.inputParameter_arg);
|
||||
NcFile f(args_info.inputParameter_arg, NcFile::read);
|
||||
NcVar *v;
|
||||
long *particle_id;
|
||||
double *expansion_fac;
|
||||
|
|
@ -500,29 +496,32 @@ void makeBoxFromParameter(SimuData *simu, SimuData* &boxed, generateMock_info& a
|
|||
boxed->time = simu->time;
|
||||
boxed->BoxSize = simu->BoxSize;
|
||||
|
||||
NcAtt *d_sub = f.get_att("data_subsampling");
|
||||
if (d_sub == 0 || d_sub->as_double(0)/args_info.subsample_arg-1. > 1.e-5)
|
||||
NcGroupAtt d_sub = f.getAtt("data_subsampling");
|
||||
auto checkAtt = [&args_info](NcGroupAtt a) {
|
||||
if (a.isNull())
|
||||
return true;
|
||||
double subsampling;
|
||||
a.getValues(&subsampling);
|
||||
return subsampling/args_info.subsample_arg - 1 > 1e-5;
|
||||
};
|
||||
if (checkAtt(d_sub))
|
||||
{
|
||||
cerr << "Parameter file was not generated with the same simulation subsampling argument. Particles will be different. Stop here." << d_sub->as_double(0) << " " << args_info.subsample_arg <<endl;
|
||||
cerr << "Parameter file was not generated with the same simulation subsampling argument. Particles will be different. Stop here." <<endl;
|
||||
exit(1);
|
||||
}
|
||||
|
||||
NcVar *v_id = f.get_var("particle_ids");
|
||||
NcVar *v_snap = f.get_var("snapshot_split");
|
||||
long *edges1;
|
||||
long *dim_snap;
|
||||
NcVar v_id = f.getVar("particle_ids");
|
||||
NcVar v_snap = f.getVar("snapshot_split");
|
||||
double *ranges;
|
||||
double *mul;
|
||||
|
||||
edges1 = v_id->edges();
|
||||
dim_snap = v_snap->edges();
|
||||
assert(v_id->num_dims()==1);
|
||||
assert(v_snap->num_dims()==1);
|
||||
std::vector<NcDim> edges1 = v_id.getDims();
|
||||
std::vector<NcDim> dim_snap = v_snap.getDims();
|
||||
assert(edges1.size()==1);
|
||||
assert(dim_snap.size()==1);
|
||||
|
||||
boxed->NumPart = edges1[0];
|
||||
*num_snapshots = dim_snap[0];
|
||||
delete[] dim_snap;
|
||||
delete[] edges1;
|
||||
boxed->NumPart = edges1[0].getSize();
|
||||
*num_snapshots = dim_snap[0].getSize();
|
||||
|
||||
particle_id = new long[boxed->NumPart];
|
||||
uniqueID = new long[boxed->NumPart];
|
||||
|
|
@ -540,15 +539,15 @@ void makeBoxFromParameter(SimuData *simu, SimuData* &boxed, generateMock_info& a
|
|||
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);
|
||||
v_id.getVar(particle_id);
|
||||
v_snap.getVar(snapshot_split);
|
||||
|
||||
ranges[0] = f.get_att("range_x_min")->as_double(0);
|
||||
ranges[1] = f.get_att("range_x_max")->as_double(0);
|
||||
ranges[2] = f.get_att("range_y_min")->as_double(0);
|
||||
ranges[3] = f.get_att("range_y_max")->as_double(0);
|
||||
ranges[4] = f.get_att("range_z_min")->as_double(0);
|
||||
ranges[5] = f.get_att("range_z_max")->as_double(0);
|
||||
f.getAtt("range_x_min").getValues(&ranges[0]);
|
||||
f.getAtt("range_x_max").getValues(&ranges[1]);
|
||||
f.getAtt("range_y_min").getValues(&ranges[2]);
|
||||
f.getAtt("range_y_max").getValues(&ranges[3]);
|
||||
f.getAtt("range_z_min").getValues(&ranges[4]);
|
||||
f.getAtt("range_z_max").getValues(&ranges[5]);
|
||||
|
||||
for (int j = 0; j < 3; j++)
|
||||
{
|
||||
|
|
@ -559,17 +558,17 @@ void makeBoxFromParameter(SimuData *simu, SimuData* &boxed, generateMock_info& a
|
|||
}
|
||||
|
||||
uint32_t k = 0;
|
||||
NcVar *v_uniq_lsb = f.get_var("unique_ids_lsb");
|
||||
NcVar *v_uniq_msb = f.get_var("unique_ids_lsb");
|
||||
NcVar v_uniq_lsb = f.getVar("unique_ids_lsb");
|
||||
NcVar v_uniq_msb = f.getVar("unique_ids_lsb");
|
||||
nclong *tmp_int;
|
||||
|
||||
tmp_int = new nclong[boxed->NumPart];
|
||||
|
||||
v_uniq_lsb->get(tmp_int, boxed->NumPart);
|
||||
v_uniq_lsb.getVar(tmp_int);
|
||||
for (long i = 0; i < boxed->NumPart; i++)
|
||||
uniqueID[i] = tmp_int[i];
|
||||
|
||||
v_uniq_msb->get(tmp_int, boxed->NumPart);
|
||||
v_uniq_msb.getVar(tmp_int);
|
||||
for (long i = 0; i < boxed->NumPart; i++)
|
||||
uniqueID[i] |= (unsigned long)(tmp_int[i]) << 32;
|
||||
|
||||
|
|
|
|||
|
|
@ -37,3 +37,5 @@ target_link_libraries(pruneVoids ${ZOB_LIBS})
|
|||
#add_genopt(makeAHFOutput_SRCS makeAHFOutput.ggo makeAHFOutput_conf STRUCTNAME makeAHFOutput_info)
|
||||
#add_executable(makeAHFOutput ${makeAHFOutput_SRCS})
|
||||
#target_link_libraries(makeAHFOutput ${ZOB_LIBS})
|
||||
|
||||
install(TARGETS pruneVoids DESTINATION ${VIDE_BIN})
|
||||
|
|
|
|||
|
|
@ -37,7 +37,7 @@
|
|||
#include "stdlib.h"
|
||||
#include <math.h>
|
||||
#include <stdio.h>
|
||||
#include <netcdfcpp.h>
|
||||
#include <netcdf>
|
||||
#include "pruneVoids_conf.h"
|
||||
#include <vector>
|
||||
#include "assert.h"
|
||||
|
|
@ -243,13 +243,13 @@ int main(int argc, char **argv) {
|
|||
|
||||
// load box size
|
||||
printf("\n Getting info...\n");
|
||||
NcFile f_info(args.extraInfo_arg);
|
||||
ranges[0][0] = f_info.get_att("range_x_min")->as_double(0);
|
||||
ranges[0][1] = f_info.get_att("range_x_max")->as_double(0);
|
||||
ranges[1][0] = f_info.get_att("range_y_min")->as_double(0);
|
||||
ranges[1][1] = f_info.get_att("range_y_max")->as_double(0);
|
||||
ranges[2][0] = f_info.get_att("range_z_min")->as_double(0);
|
||||
ranges[2][1] = f_info.get_att("range_z_max")->as_double(0);
|
||||
netCDF::NcFile f_info(args.extraInfo_arg, netCDF::NcFile::read);
|
||||
f_info.getAtt("range_x_min").getValues(&ranges[0][0]);
|
||||
f_info.getAtt("range_x_max").getValues(&ranges[0][1]);
|
||||
f_info.getAtt("range_y_min").getValues(&ranges[1][0]);
|
||||
f_info.getAtt("range_y_max").getValues(&ranges[1][1]);
|
||||
f_info.getAtt("range_z_min").getValues(&ranges[2][0]);
|
||||
f_info.getAtt("range_z_max").getValues(&ranges[2][1]);
|
||||
|
||||
printf(" Range xmin %e\n", ranges[0][0]);
|
||||
printf(" Range xmax %e\n", ranges[0][1]);
|
||||
|
|
|
|||
|
|
@ -22,3 +22,5 @@ if (ENABLE_OPENMP)
|
|||
omp_add_flags(jozov2 CXX)
|
||||
add_definitions(-DOPENMP)
|
||||
ENDIF(ENABLE_OPENMP)
|
||||
|
||||
install(TARGETS jozov2 DESTINATION ${VIDE_BIN})
|
||||
|
|
|
|||
|
|
@ -1,4 +1,5 @@
|
|||
add_executable(voz1b1_2 voz1b1.cpp vozutil.c voz_io.cpp)
|
||||
target_link_libraries(voz1b1_2 ${QHULL_LIBRARY} ${COSMOTOOL_LIBRARY} ${MATH_LIB})
|
||||
|
||||
install(TARGETS voz1b1_2 DESTINATION ${VIDE_BIN})
|
||||
include_directories(${COSMOTOOL_INCLUDE_PATH} ${QHULL_INCLUDE_PATH})
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue