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renamed 'generateMock' routines to 'prep' routines to accurately reflect what they do

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This commit is contained in:
Paul M. Sutter 2024-05-22 15:46:04 -04:00
parent b1962100a8
commit 50ad2d6d73
21 changed files with 69 additions and 89 deletions
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26
.gitignore vendored
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@ -54,28 +54,12 @@ c_tools/mock/loaders/CMakeFiles/
c_tools/mock/loaders/Makefile c_tools/mock/loaders/Makefile
c_tools/mock/loaders/cmake_install.cmake c_tools/mock/loaders/cmake_install.cmake
c_tools/mock/loaders/libsimu_loaders.a c_tools/mock/loaders/libsimu_loaders.a
c_tools/stacking/CMakeFiles/ c_tools/pruning/CMakeFiles/
c_tools/stacking/Makefile c_tools/pruning/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/stacking/dumpVoidParticles.c c_tools/stacking/dumpVoidParticles.c
c_tools/stacking/pruneVoids c_tools/pruning/pruneVoids
c_tools/stacking/pruneVoids_conf.c c_tools/pruning/pruneVoids_conf.c
c_tools/stacking/pruneVoids_conf.h c_tools/pruning/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/test/CMakeFiles/ c_tools/test/CMakeFiles/
c_tools/test/Makefile c_tools/test/Makefile
c_tools/test/cmake_install.cmake c_tools/test/cmake_install.cmake

2
c_tools/CMakeLists.txt
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@ -45,4 +45,4 @@ add_genopt(computeAverageDistortion_SRCS computeAverageDistortion.ggo computeAve
#add_executable(computeAverageDistortion ${computeAverageDistortion_SRCS}) #add_executable(computeAverageDistortion ${computeAverageDistortion_SRCS})
#target_link_libraries(computeAverageDistortion ${ZOB_LIBS}) #target_link_libraries(computeAverageDistortion ${ZOB_LIBS})
subdirs(libzobov mock pruning jozov2) subdirs(libzobov prep pruning jozov2)

26
c_tools/mock/CMakeLists.txt
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@ -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})

22
c_tools/prep/CMakeLists.txt Normal file
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@ -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})

0
c_tools/mock/generateTestMock.cpp → c_tools/prep/generateMock.cpp
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0
c_tools/mock/loaders/CMakeLists.txt → c_tools/prep/loaders/CMakeLists.txt
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0
c_tools/mock/loaders/basic_loader.cpp → c_tools/prep/loaders/basic_loader.cpp
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0
c_tools/mock/loaders/flash_loader.cpp → c_tools/prep/loaders/flash_loader.cpp
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0
c_tools/mock/loaders/gadget_loader.cpp → c_tools/prep/loaders/gadget_loader.cpp
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0
c_tools/mock/loaders/multidark_loader.cpp → c_tools/prep/loaders/multidark_loader.cpp
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0
c_tools/mock/loaders/ramses_loader.cpp → c_tools/prep/loaders/ramses_loader.cpp
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0
c_tools/mock/loaders/sdf_loader.cpp → c_tools/prep/loaders/sdf_loader.cpp
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0
c_tools/mock/loaders/sdfloader_internal.hpp → c_tools/prep/loaders/sdfloader_internal.hpp
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0
c_tools/mock/loaders/simulation_loader.cpp → c_tools/prep/loaders/simulation_loader.cpp
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0
c_tools/mock/loaders/simulation_loader.hpp → c_tools/prep/loaders/simulation_loader.hpp
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26
c_tools/mock/generateFromCatalog.cpp → c_tools/prep/prepObservation.cpp
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@ -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) 2010-2014 Guilhem Lavaux
Copyright (C) 2011-2014 P. M. Sutter Copyright (C) 2011-2014 P. M. Sutter
@ -26,7 +26,7 @@
#include <fstream> #include <fstream>
#include <vector> #include <vector>
#include <string> #include <string>
#include "generateFromCatalog_conf.h" #include "prepObservation_conf.h"
#include "contour_pixels.hpp" #include "contour_pixels.hpp"
#include <netcdf> #include <netcdf>
#include <CosmoTool/fortran.hpp> #include <CosmoTool/fortran.hpp>
@ -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) bool useComoving, double omegaM)
{ {
double d2r = M_PI/180; double d2r = M_PI/180;
@ -223,7 +223,7 @@ void generateGalaxiesInCube(NYU_VData& data, ParticleData& output_data,
gsl_interp_free(interp); gsl_interp_free(interp);
} }
void generateSurfaceMask(generateFromCatalog_info& args , void generateSurfaceMask(prepObservation_info& args ,
Healpix_Map<float>& mask, Healpix_Map<float>& mask,
vector<int>& pixel_list, vector<int>& pixel_list,
vector<int>& full_mask_list, vector<int>& full_mask_list,
@ -577,32 +577,32 @@ void saveForZobov(ParticleData& pdata, const string& fname, const string& paramn
int main(int argc, char **argv) int main(int argc, char **argv)
{ {
generateFromCatalog_info args_info; prepObservation_info args_info;
generateFromCatalog_conf_params args_params; prepObservation_conf_params args_params;
generateFromCatalog_conf_init(&args_info); prepObservation_conf_init(&args_info);
generateFromCatalog_conf_params_init(&args_params); prepObservation_conf_params_init(&args_params);
args_params.check_required = 0; 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; return 1;
if (!args_info.configFile_given) 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; return 1;
} }
else else
{ {
args_params.check_required = 1; args_params.check_required = 1;
args_params.initialize = 0; 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_info,
&args_params)) &args_params))
return 1; return 1;
} }
generateFromCatalog_conf_print_version(); prepObservation_conf_print_version();
cout << "Loading data " << args_info.catalog_arg << "..." << endl; cout << "Loading data " << args_info.catalog_arg << "..." << endl;
vector<NYU_Data> data; vector<NYU_Data> data;
@ -628,7 +628,7 @@ int main(int argc, char **argv)
// We compute a cube holding all the galaxies + the survey surface mask // We compute a cube holding all the galaxies + the survey surface mask
cout << "Placing galaxies..." << endl; cout << "Placing galaxies..." << endl;
generateGalaxiesInCube(data, output_data, args_info.useComoving_flag, placeGalaxiesInCube(data, output_data, args_info.useComoving_flag,
args_info.omegaM_arg); args_info.omegaM_arg);
generateSurfaceMask(args_info, mask, pixel_list, full_mask_list, generateSurfaceMask(args_info, mask, pixel_list, full_mask_list,
data, output_data,args_info.useComoving_flag, data, output_data,args_info.useComoving_flag,

2
c_tools/mock/generateFromCatalog.ggo → c_tools/prep/prepObservation.ggo
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@ -1,4 +1,4 @@
package "generateFromCatalog" package "prepObservation"
version "alpha" version "alpha"
option "configFile" - "Configuration filename" string optional option "configFile" - "Configuration filename" string optional

30
c_tools/mock/generateMock.cpp → c_tools/prep/prepSimulation.cpp
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@ -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) 2010-2014 Guilhem Lavaux
Copyright (C) 2011-2014 P. M. Sutter Copyright (C) 2011-2014 P. M. Sutter
@ -34,7 +34,7 @@
#include <CosmoTool/interpolate.hpp> #include <CosmoTool/interpolate.hpp>
#include <CosmoTool/fortran.hpp> #include <CosmoTool/fortran.hpp>
#include <CosmoTool/algo.hpp> #include <CosmoTool/algo.hpp>
#include "generateMock_conf.h" #include "prepSimulation_conf.h"
#include "gslIntegrate.hpp" #include "gslIntegrate.hpp"
#include <netcdf> #include <netcdf>
#include "simulation_loader.hpp" #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 // 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. // 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, SimulationPreprocessor *preselect) void selectBox(SimuData *simu, std::vector<long>& targets, prepSimulation_info& args_info, SimulationPreprocessor *preselect)
{ {
double ranges[3][2] = { double ranges[3][2] = {
{ args_info.rangeX_min_arg, args_info.rangeX_max_arg }, { args_info.rangeX_min_arg, args_info.rangeX_max_arg },
@ -331,7 +331,7 @@ public:
} }
}; };
void createBox(SimuData *simu, vector<long>& targets, vector<long>& snapshot_split, SimuData *& boxed, generateMock_info& args_info) void createBox(SimuData *simu, vector<long>& targets, vector<long>& snapshot_split, SimuData *& boxed, prepSimulation_info& args_info)
{ {
double *ranges = new double[6]; double *ranges = new double[6];
double *mul = new double[3]; 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<double>("ranges"); double *ranges = boxed->as<double>("ranges");
NcFile f(outbox.c_str(), NcFile::replace); 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); 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); NcFile f(args_info.inputParameter_arg, NcFile::read);
NcVar *v; 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; 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<long> targets, split; vector<long> targets, split;
long previous_target_num = 0; long previous_target_num = 0;
@ -647,34 +647,34 @@ void makeBoxFromSimulation(SimulationLoader *loader, SimuData* &boxed, MetricFun
int main(int argc, char **argv) int main(int argc, char **argv)
{ {
generateMock_info args_info; prepSimulation_info args_info;
generateMock_conf_params args_params; prepSimulation_conf_params args_params;
SimuData *simu, *simuOut; SimuData *simu, *simuOut;
SimulationLoader *loader; SimulationLoader *loader;
generateMock_conf_init(&args_info); prepSimulation_conf_init(&args_info);
generateMock_conf_params_init(&args_params); prepSimulation_conf_params_init(&args_params);
args_params.check_required = 0; 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; return 1;
if (!args_info.configFile_given) 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; return 1;
} }
else else
{ {
args_params.check_required = 1; args_params.check_required = 1;
args_params.initialize = 0; 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_info,
&args_params)) &args_params))
return 1; return 1;
} }
generateMock_conf_print_version(); prepSimulation_conf_print_version();
SimulationPreprocessor *preselector = new PreselectParticles(args_info.subsample_arg, args_info.subsample_seed_arg); SimulationPreprocessor *preselector = new PreselectParticles(args_info.subsample_arg, args_info.subsample_seed_arg);

2
c_tools/mock/generateMock.ggo → c_tools/prep/prepSimulation.ggo
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@ -1,4 +1,4 @@
package "generateMock" package "prepSimulation"
version "0" version "0"
option "configFile" - "Configuration file path" string optional option "configFile" - "Configuration file path" string optional

6
python_tools/vide/backend/launchers.py
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@ -46,9 +46,9 @@ ncFloat = 'f8' # Double precision
LIGHT_SPEED = 299792.458 LIGHT_SPEED = 299792.458
# ----------------------------------------------------------------------------- # -----------------------------------------------------------------------------
def launchGenerate(sample, binPath, workDir=None, inputDataDir=None, def launchPrep(sample, binPath, workDir=None, inputDataDir=None,
zobovDir=None, figDir=None, logFile=None, useComoving=False, zobovDir=None, figDir=None, logFile=None, useComoving=False,
continueRun=None,regenerate=False): continueRun=None,regenerate=False):
if sample.dataType == "observation": if sample.dataType == "observation":
sampleName = sample.fullName sampleName = sample.fullName

16
python_tools/void_pipeline/__main__.py
View file

@ -19,7 +19,7 @@
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. # 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 2 : find voids
# Stage 3 : prune catalog # Stage 3 : prune catalog
@ -89,14 +89,14 @@ for sample in dataSampleList:
logFile = logDir+"/generate_"+sampleName+".out" logFile = logDir+"/generate_"+sampleName+".out"
if sample.dataType == "observation": if sample.dataType == "observation":
GENERATE_PATH = CTOOLS_PATH+"/generateFromCatalog" GENERATE_PATH = CTOOLS_PATH+"/prepObservation"
else: else:
GENERATE_PATH = CTOOLS_PATH+"/generateMock" GENERATE_PATH = CTOOLS_PATH+"/prepSimulation"
launchGenerate(sample, GENERATE_PATH, workDir=workDir, launchPrep(sample, GENERATE_PATH, workDir=workDir,
inputDataDir=inputDataDir, zobovDir=zobovDir, inputDataDir=inputDataDir, zobovDir=zobovDir,
figDir=figDir, logFile=logFile, useComoving=sample.useComoving, figDir=figDir, logFile=logFile, useComoving=sample.useComoving,
continueRun=continueRun, regenerate=regenerateFlag) continueRun=continueRun, regenerate=regenerateFlag)
# -------------------------------------------------------------------------- # --------------------------------------------------------------------------
if (startCatalogStage <= 2) and (endCatalogStage >= 2) and not sample.isCombo: 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: if (startCatalogStage <= 3) and (endCatalogStage >= 3) and not sample.isCombo:
print(" Taking data portions", "...", end=' ') print(" Pruning void catalogs", "...", end=' ')
sys.stdout.flush() sys.stdout.flush()
logFile = logDir+"/pruneVoids_"+sampleName+".out" logFile = logDir+"/pruneVoids_"+sampleName+".out"