diff --git a/.gitignore b/.gitignore index 6b6572e..9e01266 100644 --- a/.gitignore +++ b/.gitignore @@ -54,28 +54,12 @@ c_tools/mock/loaders/CMakeFiles/ c_tools/mock/loaders/Makefile c_tools/mock/loaders/cmake_install.cmake c_tools/mock/loaders/libsimu_loaders.a -c_tools/stacking/CMakeFiles/ -c_tools/stacking/Makefile -c_tools/stacking/cmake_install.cmake -c_tools/stacking/computeVelocityProfile -c_tools/stacking/computeVelocityProfile_conf.c -c_tools/stacking/computeVelocityProfile_conf.h +c_tools/pruning/CMakeFiles/ +c_tools/pruning/Makefile c_tools/stacking/dumpVoidParticles.c -c_tools/stacking/pruneVoids -c_tools/stacking/pruneVoids_conf.c -c_tools/stacking/pruneVoids_conf.h -c_tools/stacking/stackDensityField -c_tools/stacking/stackDensityField_conf.c -c_tools/stacking/stackDensityField_conf.h -c_tools/stacking/stackVelocityField -c_tools/stacking/stackVelocityField_conf.c -c_tools/stacking/stackVelocityField_conf.h -c_tools/stacking/stackVoids -c_tools/stacking/stackVoidsZero -c_tools/stacking/stackVoidsZero_conf.c -c_tools/stacking/stackVoidsZero_conf.h -c_tools/stacking/stackVoids_conf.c -c_tools/stacking/stackVoids_conf.h +c_tools/pruning/pruneVoids +c_tools/pruning/pruneVoids_conf.c +c_tools/pruning/pruneVoids_conf.h c_tools/test/CMakeFiles/ c_tools/test/Makefile c_tools/test/cmake_install.cmake diff --git a/c_tools/CMakeLists.txt b/c_tools/CMakeLists.txt index 487fad3..2ac81ab 100644 --- a/c_tools/CMakeLists.txt +++ b/c_tools/CMakeLists.txt @@ -45,4 +45,4 @@ add_genopt(computeAverageDistortion_SRCS computeAverageDistortion.ggo computeAve #add_executable(computeAverageDistortion ${computeAverageDistortion_SRCS}) #target_link_libraries(computeAverageDistortion ${ZOB_LIBS}) -subdirs(libzobov mock pruning jozov2) +subdirs(libzobov prep pruning jozov2) diff --git a/c_tools/mock/CMakeLists.txt b/c_tools/mock/CMakeLists.txt deleted file mode 100644 index a5d25d2..0000000 --- a/c_tools/mock/CMakeLists.txt +++ /dev/null @@ -1,26 +0,0 @@ -include_directories(${CMAKE_CURRENT_BINARY_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/loaders) - -IF(SDF_SUPPORT) - add_definitions(-DSDF_SUPPORT) -ENDIF(SDF_SUPPORT) - -SET(generateMock_SRCS generateMock.cpp ) -add_genopt(generateMock_SRCS generateMock.ggo generateMock_conf STRUCTNAME generateMock_info) -add_executable(generateMock ${generateMock_SRCS}) -target_link_libraries(generateMock simu_loaders ${ZOB_LIBS} ${LIBSDF_LIBRARY} ${HDF5_CXX_LIBRARIES} ${HDF5_HL_LIBRARIES} ${HDF5_LIBRARIES} ${DL_LIBRARY}) - -add_executable(generateTestMock generateTestMock.cpp) -target_link_libraries(generateTestMock ${ZOB_LIBS}) - - -SET(generateFromCatalog_SRCS generateFromCatalog.cpp) -add_genopt(generateFromCatalog_SRCS generateFromCatalog.ggo generateFromCatalog_conf STRUCTNAME generateFromCatalog_info) -add_executable(generateFromCatalog ${generateFromCatalog_SRCS}) -target_link_libraries(generateFromCatalog ${ZOB_LIBS} ${HDF5_CXX_LIBRARIES} ${HDF5_HL_LIBRARIES} ${HDF5_LIBRARIES} ${HEALPIX_LIBRARIES} ${DL_LIBRARY}) - -set_target_properties(generateFromCatalog PROPERTIES COMPILE_FLAGS ${OpenMP_CXX_FLAGS} LINK_FLAGS ${OpenMP_CXX_FLAGS}) - -subdirs(loaders) - -install(TARGETS generateMock generateTestMock generateFromCatalog DESTINATION ${VIDE_BIN}) - diff --git a/c_tools/prep/CMakeLists.txt b/c_tools/prep/CMakeLists.txt new file mode 100644 index 0000000..ee566d4 --- /dev/null +++ b/c_tools/prep/CMakeLists.txt @@ -0,0 +1,22 @@ +include_directories(${CMAKE_CURRENT_BINARY_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/loaders) + +IF(SDF_SUPPORT) + add_definitions(-DSDF_SUPPORT) +ENDIF(SDF_SUPPORT) + +SET(prepSimulation_SRCS prepSimulation.cpp ) +add_genopt(prepSimulation_SRCS prepSimulation.ggo prepSimulation_conf STRUCTNAME prepSimulation_info) +add_executable(prepSimulation ${prepSimulation_SRCS}) +target_link_libraries(prepSimulation simu_loaders ${ZOB_LIBS} ${LIBSDF_LIBRARY} ${HDF5_CXX_LIBRARIES} ${HDF5_HL_LIBRARIES} ${HDF5_LIBRARIES} ${DL_LIBRARY}) + +SET(prepObservation_SRCS prepObservation.cpp) +add_genopt(prepObservation_SRCS prepObservation.ggo prepObservation_conf STRUCTNAME prepObservation_info) +add_executable(prepObservation ${prepObservation_SRCS}) +target_link_libraries(prepObservation ${ZOB_LIBS} ${HDF5_CXX_LIBRARIES} ${HDF5_HL_LIBRARIES} ${HDF5_LIBRARIES} ${HEALPIX_LIBRARIES} ${DL_LIBRARY}) + +set_target_properties(prepObservation PROPERTIES COMPILE_FLAGS ${OpenMP_CXX_FLAGS} LINK_FLAGS ${OpenMP_CXX_FLAGS}) + +subdirs(loaders) + +install(TARGETS prepSimulation prepObservation DESTINATION ${VIDE_BIN}) + diff --git a/c_tools/mock/generateTestMock.cpp b/c_tools/prep/generateMock.cpp similarity index 100% rename from c_tools/mock/generateTestMock.cpp rename to c_tools/prep/generateMock.cpp diff --git a/c_tools/mock/loaders/CMakeLists.txt b/c_tools/prep/loaders/CMakeLists.txt similarity index 100% rename from c_tools/mock/loaders/CMakeLists.txt rename to c_tools/prep/loaders/CMakeLists.txt diff --git a/c_tools/mock/loaders/basic_loader.cpp b/c_tools/prep/loaders/basic_loader.cpp similarity index 100% rename from c_tools/mock/loaders/basic_loader.cpp rename to c_tools/prep/loaders/basic_loader.cpp diff --git a/c_tools/mock/loaders/flash_loader.cpp b/c_tools/prep/loaders/flash_loader.cpp similarity index 100% rename from c_tools/mock/loaders/flash_loader.cpp rename to c_tools/prep/loaders/flash_loader.cpp diff --git a/c_tools/mock/loaders/gadget_loader.cpp b/c_tools/prep/loaders/gadget_loader.cpp similarity index 100% rename from c_tools/mock/loaders/gadget_loader.cpp rename to c_tools/prep/loaders/gadget_loader.cpp diff --git a/c_tools/mock/loaders/multidark_loader.cpp b/c_tools/prep/loaders/multidark_loader.cpp similarity index 100% rename from c_tools/mock/loaders/multidark_loader.cpp rename to c_tools/prep/loaders/multidark_loader.cpp diff --git a/c_tools/mock/loaders/ramses_loader.cpp b/c_tools/prep/loaders/ramses_loader.cpp similarity index 100% rename from c_tools/mock/loaders/ramses_loader.cpp rename to c_tools/prep/loaders/ramses_loader.cpp diff --git a/c_tools/mock/loaders/sdf_loader.cpp b/c_tools/prep/loaders/sdf_loader.cpp similarity index 100% rename from c_tools/mock/loaders/sdf_loader.cpp rename to c_tools/prep/loaders/sdf_loader.cpp diff --git a/c_tools/mock/loaders/sdfloader_internal.hpp b/c_tools/prep/loaders/sdfloader_internal.hpp similarity index 100% rename from c_tools/mock/loaders/sdfloader_internal.hpp rename to c_tools/prep/loaders/sdfloader_internal.hpp diff --git a/c_tools/mock/loaders/simulation_loader.cpp b/c_tools/prep/loaders/simulation_loader.cpp similarity index 100% rename from c_tools/mock/loaders/simulation_loader.cpp rename to c_tools/prep/loaders/simulation_loader.cpp diff --git a/c_tools/mock/loaders/simulation_loader.hpp b/c_tools/prep/loaders/simulation_loader.hpp similarity index 100% rename from c_tools/mock/loaders/simulation_loader.hpp rename to c_tools/prep/loaders/simulation_loader.hpp diff --git a/c_tools/mock/generateFromCatalog.cpp b/c_tools/prep/prepObservation.cpp similarity index 95% rename from c_tools/mock/generateFromCatalog.cpp rename to c_tools/prep/prepObservation.cpp index b98a18c..ec72a0f 100644 --- a/c_tools/mock/generateFromCatalog.cpp +++ b/c_tools/prep/prepObservation.cpp @@ -1,5 +1,5 @@ /*+ - VIDE -- Void IDentification and Examination -- ./c_tools/mock/generateFromCatalog.cpp + VIDE -- Void IDentification and Examination -- ./c_tools/mock/prepObservation.cpp Copyright (C) 2010-2014 Guilhem Lavaux Copyright (C) 2011-2014 P. M. Sutter @@ -26,7 +26,7 @@ #include #include #include -#include "generateFromCatalog_conf.h" +#include "prepObservation_conf.h" #include "contour_pixels.hpp" #include #include @@ -121,7 +121,7 @@ void loadData(const string& fname, NYU_VData & data) } } -void generateGalaxiesInCube(NYU_VData& data, ParticleData& output_data, +void placeGalaxiesInCube(NYU_VData& data, ParticleData& output_data, bool useComoving, double omegaM) { double d2r = M_PI/180; @@ -223,7 +223,7 @@ void generateGalaxiesInCube(NYU_VData& data, ParticleData& output_data, gsl_interp_free(interp); } -void generateSurfaceMask(generateFromCatalog_info& args , +void generateSurfaceMask(prepObservation_info& args , Healpix_Map& mask, vector& pixel_list, vector& full_mask_list, @@ -577,32 +577,32 @@ void saveForZobov(ParticleData& pdata, const string& fname, const string& paramn int main(int argc, char **argv) { - generateFromCatalog_info args_info; - generateFromCatalog_conf_params args_params; + prepObservation_info args_info; + prepObservation_conf_params args_params; - generateFromCatalog_conf_init(&args_info); - generateFromCatalog_conf_params_init(&args_params); + prepObservation_conf_init(&args_info); + prepObservation_conf_params_init(&args_params); args_params.check_required = 0; - if (generateFromCatalog_conf_ext (argc, argv, &args_info, &args_params)) + if (prepObservation_conf_ext (argc, argv, &args_info, &args_params)) return 1; if (!args_info.configFile_given) { - if (generateFromCatalog_conf_required (&args_info, GENERATEFROMCATALOG_CONF_PACKAGE)) + if (prepObservation_conf_required (&args_info, PREPOBSERVATION_CONF_PACKAGE)) return 1; } else { args_params.check_required = 1; args_params.initialize = 0; - if (generateFromCatalog_conf_config_file (args_info.configFile_arg, + if (prepObservation_conf_config_file (args_info.configFile_arg, &args_info, &args_params)) return 1; } - generateFromCatalog_conf_print_version(); + prepObservation_conf_print_version(); cout << "Loading data " << args_info.catalog_arg << "..." << endl; vector data; @@ -628,7 +628,7 @@ int main(int argc, char **argv) // We compute a cube holding all the galaxies + the survey surface mask cout << "Placing galaxies..." << endl; - generateGalaxiesInCube(data, output_data, args_info.useComoving_flag, + placeGalaxiesInCube(data, output_data, args_info.useComoving_flag, args_info.omegaM_arg); generateSurfaceMask(args_info, mask, pixel_list, full_mask_list, data, output_data,args_info.useComoving_flag, diff --git a/c_tools/mock/generateFromCatalog.ggo b/c_tools/prep/prepObservation.ggo similarity index 96% rename from c_tools/mock/generateFromCatalog.ggo rename to c_tools/prep/prepObservation.ggo index 169cf91..e04cf1d 100644 --- a/c_tools/mock/generateFromCatalog.ggo +++ b/c_tools/prep/prepObservation.ggo @@ -1,4 +1,4 @@ -package "generateFromCatalog" +package "prepObservation" version "alpha" option "configFile" - "Configuration filename" string optional diff --git a/c_tools/mock/generateMock.cpp b/c_tools/prep/prepSimulation.cpp similarity index 96% rename from c_tools/mock/generateMock.cpp rename to c_tools/prep/prepSimulation.cpp index e36f507..350e328 100644 --- a/c_tools/mock/generateMock.cpp +++ b/c_tools/prep/prepSimulation.cpp @@ -1,5 +1,5 @@ /*+ - VIDE -- Void IDentification and Examination -- ./c_tools/mock/generateMock.cpp + VIDE -- Void IDentification and Examination -- ./c_tools/mock/prepSimulation.cpp Copyright (C) 2010-2014 Guilhem Lavaux Copyright (C) 2011-2014 P. M. Sutter @@ -34,7 +34,7 @@ #include #include #include -#include "generateMock_conf.h" +#include "prepSimulation_conf.h" #include "gslIntegrate.hpp" #include #include "simulation_loader.hpp" @@ -267,7 +267,7 @@ void generateOutput(SimuData *data, int axis, // This function prepares the list of targets for the specified snapshot. The target list is not // cleared. That way new particles can be appended if this is a multi-file snapshot. -void selectBox(SimuData *simu, std::vector& targets, generateMock_info& args_info, SimulationPreprocessor *preselect) +void selectBox(SimuData *simu, std::vector& targets, prepSimulation_info& args_info, SimulationPreprocessor *preselect) { double ranges[3][2] = { { args_info.rangeX_min_arg, args_info.rangeX_max_arg }, @@ -331,7 +331,7 @@ public: } }; -void createBox(SimuData *simu, vector& targets, vector& snapshot_split, SimuData *& boxed, generateMock_info& args_info) +void createBox(SimuData *simu, vector& targets, vector& snapshot_split, SimuData *& boxed, prepSimulation_info& args_info) { double *ranges = new double[6]; double *mul = new double[3]; @@ -424,7 +424,7 @@ void buildBox(SimuData *simu, long num_targets, long loaded, } } -void saveBox(SimuData *&boxed, const std::string& outbox, generateMock_info& args_info) +void saveBox(SimuData *&boxed, const std::string& outbox, prepSimulation_info& args_info) { double *ranges = boxed->as("ranges"); NcFile f(outbox.c_str(), NcFile::replace); @@ -479,7 +479,7 @@ void saveBox(SimuData *&boxed, const std::string& outbox, generateMock_info& arg v8.putVar({0}, {size_t(boxed->NumPart)}, velZ); } -void makeBoxFromParameter(SimuData *simu, SimuData* &boxed, generateMock_info& args_info) +void makeBoxFromParameter(SimuData *simu, SimuData* &boxed, prepSimulation_info& args_info) { NcFile f(args_info.inputParameter_arg, NcFile::read); NcVar *v; @@ -610,7 +610,7 @@ void makeBoxFromParameter(SimuData *simu, SimuData* &boxed, generateMock_info& a cout << "Num accepted here = " << pid_write << " / input = " << pid_read << endl; } -void makeBoxFromSimulation(SimulationLoader *loader, SimuData* &boxed, MetricFunctor metric, generateMock_info& args_info) +void makeBoxFromSimulation(SimulationLoader *loader, SimuData* &boxed, MetricFunctor metric, prepSimulation_info& args_info) { vector targets, split; long previous_target_num = 0; @@ -647,34 +647,34 @@ void makeBoxFromSimulation(SimulationLoader *loader, SimuData* &boxed, MetricFun int main(int argc, char **argv) { - generateMock_info args_info; - generateMock_conf_params args_params; + prepSimulation_info args_info; + prepSimulation_conf_params args_params; SimuData *simu, *simuOut; SimulationLoader *loader; - generateMock_conf_init(&args_info); - generateMock_conf_params_init(&args_params); + prepSimulation_conf_init(&args_info); + prepSimulation_conf_params_init(&args_params); args_params.check_required = 0; - if (generateMock_conf_ext (argc, argv, &args_info, &args_params)) + if (prepSimulation_conf_ext (argc, argv, &args_info, &args_params)) return 1; if (!args_info.configFile_given) { - if (generateMock_conf_required (&args_info, GENERATEMOCK_CONF_PACKAGE)) + if (prepSimulation_conf_required (&args_info, PREPSIMULATION_CONF_PACKAGE)) return 1; } else { args_params.check_required = 1; args_params.initialize = 0; - if (generateMock_conf_config_file (args_info.configFile_arg, + if (prepSimulation_conf_config_file (args_info.configFile_arg, &args_info, &args_params)) return 1; } - generateMock_conf_print_version(); + prepSimulation_conf_print_version(); SimulationPreprocessor *preselector = new PreselectParticles(args_info.subsample_arg, args_info.subsample_seed_arg); diff --git a/c_tools/mock/generateMock.ggo b/c_tools/prep/prepSimulation.ggo similarity index 98% rename from c_tools/mock/generateMock.ggo rename to c_tools/prep/prepSimulation.ggo index f907f59..49d86d5 100644 --- a/c_tools/mock/generateMock.ggo +++ b/c_tools/prep/prepSimulation.ggo @@ -1,4 +1,4 @@ -package "generateMock" +package "prepSimulation" version "0" option "configFile" - "Configuration file path" string optional diff --git a/python_tools/vide/backend/launchers.py b/python_tools/vide/backend/launchers.py index 698df61..469311b 100644 --- a/python_tools/vide/backend/launchers.py +++ b/python_tools/vide/backend/launchers.py @@ -46,9 +46,9 @@ ncFloat = 'f8' # Double precision LIGHT_SPEED = 299792.458 # ----------------------------------------------------------------------------- -def launchGenerate(sample, binPath, workDir=None, inputDataDir=None, - zobovDir=None, figDir=None, logFile=None, useComoving=False, - continueRun=None,regenerate=False): +def launchPrep(sample, binPath, workDir=None, inputDataDir=None, + zobovDir=None, figDir=None, logFile=None, useComoving=False, + continueRun=None,regenerate=False): if sample.dataType == "observation": sampleName = sample.fullName diff --git a/python_tools/void_pipeline/__main__.py b/python_tools/void_pipeline/__main__.py index e6fa06b..1fca302 100644 --- a/python_tools/void_pipeline/__main__.py +++ b/python_tools/void_pipeline/__main__.py @@ -19,7 +19,7 @@ # 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. #+ -# Stage 1 : generate particles +# Stage 1 : prepare particles for void finding # Stage 2 : find voids # Stage 3 : prune catalog @@ -89,14 +89,14 @@ for sample in dataSampleList: logFile = logDir+"/generate_"+sampleName+".out" if sample.dataType == "observation": - GENERATE_PATH = CTOOLS_PATH+"/generateFromCatalog" + GENERATE_PATH = CTOOLS_PATH+"/prepObservation" else: - GENERATE_PATH = CTOOLS_PATH+"/generateMock" + GENERATE_PATH = CTOOLS_PATH+"/prepSimulation" - launchGenerate(sample, GENERATE_PATH, workDir=workDir, - inputDataDir=inputDataDir, zobovDir=zobovDir, - figDir=figDir, logFile=logFile, useComoving=sample.useComoving, - continueRun=continueRun, regenerate=regenerateFlag) + launchPrep(sample, GENERATE_PATH, workDir=workDir, + inputDataDir=inputDataDir, zobovDir=zobovDir, + figDir=figDir, logFile=logFile, useComoving=sample.useComoving, + continueRun=continueRun, regenerate=regenerateFlag) # -------------------------------------------------------------------------- if (startCatalogStage <= 2) and (endCatalogStage >= 2) and not sample.isCombo: @@ -110,7 +110,7 @@ for sample in dataSampleList: # ------------------------------------------------------------------------- if (startCatalogStage <= 3) and (endCatalogStage >= 3) and not sample.isCombo: - print(" Taking data portions", "...", end=' ') + print(" Pruning void catalogs", "...", end=' ') sys.stdout.flush() logFile = logDir+"/pruneVoids_"+sampleName+".out"