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

.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

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)

c_tools/mock/CMakeLists.txt

@@ -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})
-

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})
+

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 <fstream>
 #include <vector>
 #include <string>
-#include "generateFromCatalog_conf.h"
+#include "prepObservation_conf.h"
 #include "contour_pixels.hpp"
 #include <netcdf>
 #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)
 {
   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<float>& mask, 
 			 vector<int>& pixel_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)
 {
-  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<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
 
   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, 

c_tools/prep/prepObservation.ggo

@@ -1,4 +1,4 @@
-package "generateFromCatalog"
+package "prepObservation"
 version "alpha"
 
 option "configFile" - "Configuration filename" string optional

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 <CosmoTool/interpolate.hpp>
 #include <CosmoTool/fortran.hpp>
 #include <CosmoTool/algo.hpp>
-#include "generateMock_conf.h"
+#include "prepSimulation_conf.h"
 #include "gslIntegrate.hpp"
 #include <netcdf>
 #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<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] = {
     { 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 *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");
   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<long> 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);
 

c_tools/prep/prepSimulation.ggo

@@ -1,4 +1,4 @@
-package "generateMock"
+package "prepSimulation"
 version "0"
 
 option "configFile"	 -	"Configuration file path"	string optional

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

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"