preparing public version

2025-07-04 15:21:11 +00:00 · 2014-04-21 23:58:17 -04:00 · 2014-04-21 23:58:17 -04:00 · ad3e5d1577
commit ad3e5d1577
parent c57359197c
25 changed files with 934 additions and 1500 deletions
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@ -0,0 +1,89 @@
+cmake_minimum_required(VERSION 2.8)
+
+project(zobovPerso)
+
+include(CheckCCompilerFlag)
+include(ExternalProject)
+
+check_c_compiler_flag(-march=native SUPPORT_ARCH_NATIVE )
+
+
+
+find_library(MATH_LIB m)
+
+macro(add_genopt _sourcelist _ggofile _basefile)
+
+  unset(_structname)
+  unset(_funcname)
+
+  if(NOT EXISTS ${CMAKE_CURRENT_BINARY_DIR}/${_ggofile})
+    set(_ggofile2 ${CMAKE_CURRENT_SOURCE_DIR}/${_ggofile})
+  else(NOT EXISTS ${CMAKE_CURRENT_BINARY_DIR}/${_ggofile})
+    set(_ggofile2 ${CMAKE_CURRENT_BINARY_DIR}/${_ggofile})
+  endif(NOT EXISTS ${CMAKE_CURRENT_BINARY_DIR}/${_ggofile})
+
+  foreach(arg ${ARGN})
+    if ("x${arg}" MATCHES "^x(STRUCTNAME|FUNCNAME)$")
+      SET(doing "${arg}")
+    elseif(doing STREQUAL "STRUCTNAME")
+      SET(_structname ${arg})
+    elseif(doing STREQUAL "FUNCNAME")
+      SET(_funcname ${arg})
+    endif()
+  endforeach(arg ${ARGN})
+
+  if(NOT DEFINED _structname)
+    set(_structname ${_basefile})
+  endif(NOT DEFINED _structname)
+
+  if(NOT DEFINED _funcname)
+    set(_funcname ${_basefile})
+  endif(NOT DEFINED _funcname)
+  
+  set(_cfile ${CMAKE_CURRENT_BINARY_DIR}/${_basefile}.c)
+  set(_hfile ${CMAKE_CURRENT_BINARY_DIR}/${_basefile}.h)
+
+  add_custom_command(
+    OUTPUT ${_cfile} ${_hfile}
+    COMMAND ${GENGETOPT} -i ${_ggofile2} -f ${_funcname} -a ${_structname} zobovConf_info -F ${_basefile} -C
+    DEPENDS ${_ggofile2}
+    )
+
+  set(${_sourcelist} ${_cfile} ${${_sourcelist}})  
+
+endmacro(add_genopt)
+
+macro(configure_exec _source _destdir _destfile)
+
+  SET(TMP_CONFIGURE_DIR ${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY})
+  configure_file(${_source} ${TMP_CONFIGURE_DIR}/${_destfile} @ONLY)
+  file(COPY ${TMP_CONFIGURE_DIR}/${_destfile} DESTINATION ${_destdir} 
+       FILE_PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE)
+ 
+endmacro(configure_exec)
+
+include(${CMAKE_SOURCE_DIR}/external/external_build.cmake)
+include(${CMAKE_SOURCE_DIR}/external/external_python_build.cmake)
+
+SET(PYTHONPATH ${PYTHON_LOCAL_SITE_PACKAGE})
+configure_exec(${CMAKE_SOURCE_DIR}/run_python.sh.in ${CMAKE_BINARY_DIR} run_python.sh)
+configure_exec(${CMAKE_SOURCE_DIR}/run_env.sh.in  ${CMAKE_BINARY_DIR} run_env.sh)
+configure_exec(${CMAKE_SOURCE_DIR}/python_tools/pipeline_source/prepareCatalogs.in.py
+${CMAKE_BINARY_DIR}/pipeline prepareCatalogs.py)
+#configure_exec(${CMAKE_SOURCE_DIR}/python_tools/pipeline_source/applyMaskToMock.in.py
+${CMAKE_BINARY_DIR}/pipeline applyMaskToMock.py)
+#configure_exec(${CMAKE_SOURCE_DIR}/python_tools/pipeline_source/buildSkyProjections.in.py
+${CMAKE_BINARY_DIR}/pipeline/miscTools buildSkyProjections.py)
+
+SET(python_build_environment
+  ${CMAKE_COMMAND} -DPYTHON_LOCAL_SITE_PACKAGE=${PYTHON_LOCAL_SITE_PACKAGE} -DVOID_GSL=${CMAKE_BINARY_DIR}/ext_build/gsl -DPYTHON_EXECUTABLE=${PYTHON_EXECUTABLE} -DTARGET_PATH=${CMAKE_BINARY_DIR}/ext_build/python -P)
+
+add_custom_target(python_pipeline ALL
+  COMMAND ${python_build_environment} ${CMAKE_SOURCE_DIR}/external/python_build.cmake
+  COMMAND ${python_build_environment} ${CMAKE_SOURCE_DIR}/external/python_install.cmake
+  DEPENDS gsl cython netcdf4-python ${PYTHON_AUXILIARY_DEPEND}
+  WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/python_tools
+)
+
+
+subdirs(zobov c_tools)
--- a/c_tools/CMakeLists.txt
+++ b/c_tools/CMakeLists.txt
@ -0,0 +1,50 @@
+
+include(FindPkgConfig)
+
+pkg_check_modules(CAIROMM cairomm-1.0)
+pkg_check_modules(SIGC sigc++-2.0)
+pkg_check_modules(CAIRO cairo)
+pkg_check_modules(FREETYPE freetype2)
+
+find_path(CAIROMMCONFIG_INCLUDE_PATH NAMES cairommconfig.h HINTS ${CAIROMM_INCLUDE_DIRS})
+find_path(CAIROMM_INCLUDE_PATH NAMES cairomm/cairomm.h HINTS ${CAIROMM_INCLUDE_DIRS})
+find_path(SIGC_INCLUDE_PATH NAMES sigc++/slot.h HINTS ${SIGC_INCLUDE_DIRS})
+find_path(SIGCCONFIG_INCLUDE_PATH NAMES sigc++config.h HINTS ${SIGC_INCLUDE_DIRS})
+find_path(CAIRO_INCLUDE_PATH NAMES cairo.h HINTS ${CAIRO_INCLUDE_DIRS})
+find_path(FREETYPE_INCLUDE_PATH NAMES freetype/config/ftheader.h HINTS ${FREETYPE_INCLUDE_DIRS})
+
+find_library(CAIROMM_LIB NAMES ${CAIROMM_LIBRARIES} HINTS CAIROMM_LIBRARY_DIRS)
+
+IF (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)
+
+  SET(CAIRO_FOUND 1)
+  SET(ALL_CAIROMM_LIBS ${CAIROMM_LIB})
+  SET(CAIRO_HEADERS ${CAIROMM_INCLUDE_PATH} 
+    ${CAIROMMCONFIG_INCLUDE_PATH} ${SIGC_INCLUDE_PATH} 
+    ${SIGCCONFIG_INCLUDE_PATH} ${CAIRO_INCLUDE_PATH}
+    ${FREETYPE_INCLUDE_PATH})
+
+ELSE (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)
+
+  SET(CAIRO_FOUND 0)
+
+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)
+
+SET(ZOB_LIBS zobovTool 
+  ${COSMOTOOL_LIBRARY} ${GSL_LIBRARIES}
+  ${NETCDF_LIBRARIES})
+
+
+include_directories(
+  ${QHULL_INCLUDES}
+  ${HEALPIX_INCLUDE_PATH}
+  ${CMAKE_CURRENT_BINARY_DIR}
+  ${CMAKE_CURRENT_SOURCE_DIR}/libzobov)
+
+
+set(computeAverageDistortion_SRCS computeAverageDistortion.cpp)
+add_genopt(computeAverageDistortion_SRCS computeAverageDistortion.ggo computeAverageDistortion_conf STRUCTNAME Params)
+add_executable(computeAverageDistortion ${computeAverageDistortion_SRCS})
+target_link_libraries(computeAverageDistortion ${ZOB_LIBS})
+
+subdirs(libzobov test mock  stacking visualization analysis zobov2 hod)
--- a/c_tools/analysis/CMakeLists.txt
+++ b/c_tools/analysis/CMakeLists.txt
@ -0,0 +1,6 @@
+include_directories(${CMAKE_CURRENT_BINARY_DIR})
+
+SET(voidOverlap_SRCS voidOverlap.cpp)
+add_genopt(voidOverlap_SRCS voidOverlap.ggo voidOverlap_conf STRUCTNAME voidOverlap_info)
+add_executable(voidOverlap ${voidOverlap_SRCS})
+target_link_libraries(voidOverlap  ${ZOB_LIBS})
--- a/c_tools/hod/CMakeLists.txt
+++ b/c_tools/hod/CMakeLists.txt
@ -0,0 +1,21 @@
+include_directories(${CMAKE_CURRENT_BINARY_DIR})
+
+SET(hod_SRCS header.c main.c utility.c sigmac.c transfnc.c transfunc_file.c 
+  nonlinear_power_spectrum.c least_squares.c hod_functions.c 
+   xi_matter.c one_halo_rspace.c two_halo_rspace.c 
+  input_params.c dFdx.c mstar.c halo_concentration.c growthfactor.c 
+  halo_mass_conversion.c nfw_transform.c 
+  pair_density.c tasks.c wp_minimization.c 
+  kaiser_distortions.c 
+  tf_eisenstein_hu.c  jeans.c
+  populate_simulation.c test.c
+  dark_matter_statistics.c 
+  meshlink2.c nbrsfind2.c i3tensor_2.c 
+  mcmc.c halo_mass_function.c halo_bias.c
+  nrutil.c qromo.c midpnt.c midinf.c polint.c splint.c spline.c 
+  zbrent.c qtrap.c trapzd.c cisi.c complex.c amoeba.c amotry.c 
+  gaussj.c powell.c linmin.c f1dim.c mnbrak.c brent.c gasdev.c 
+  ran1.c jacobi.c splin2.c splie2.c ran2.c sort2.c
+)
+add_executable(hod ${hod_SRCS})
+target_link_libraries(hod  -lm)
--- a/c_tools/hod/users_manual.pdf
+++ b/c_tools/hod/users_manual.pdf
--- a/c_tools/libzobov/CMakeLists.txt
+++ b/c_tools/libzobov/CMakeLists.txt
@ -0,0 +1,8 @@
+
+add_library(zobovTool loadZobov.cpp particleInfo.cpp contour_pixels.cpp)
+
+set_target_properties(zobovTool PROPERTIES COMPILE_FLAGS ${OpenMP_CXX_FLAGS} LINK_FLAGS ${OpenMP_CXX_FLAGS})
+
+SET(ZOB_LIBS zobovTool ${COSMOTOOL_LIBRARY} ${GSL_LIBRARY} ${GSLCBLAS_LIBRARY} ${NETCDFCPP_LIBRARY} ${NETCDF_LIBRARY})
+SET(ZOB_LIBS PARENT ${ZOB_LIBS})
+
--- a/c_tools/mock/CMakeLists.txt
+++ b/c_tools/mock/CMakeLists.txt
@ -0,0 +1,23 @@
+include_directories(${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} ${HDF5HL_CPP_LIBRARY} ${HDF5_CPP_LIBRARY} ${HDF5_LIBRARY} ${LIBSDF_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} ${HDF5HL_CPP_LIBRARY} ${HDF5_CPP_LIBRARY} ${HEALPIX_LIBRARIES})
+
+set_target_properties(generateFromCatalog PROPERTIES COMPILE_FLAGS ${OpenMP_CXX_FLAGS} LINK_FLAGS ${OpenMP_CXX_FLAGS})
+
+subdirs(loaders)
--- a/c_tools/mock/loaders/CMakeLists.txt
+++ b/c_tools/mock/loaders/CMakeLists.txt
@ -0,0 +1,11 @@
+SET(SIMU_LOADERS_SRCS 
+   simulation_loader.cpp ramses_loader.cpp 
+   gadget_loader.cpp flash_loader.cpp)
+
+IF (SDF_SUPPORT)
+ add_definitions(-DSDF_SUPPORT)
+ SET(SIMU_LOADERS_SRCS ${SIMU_LOADERS_SRCS} sdf_loader.cpp multidark_loader.cpp)
+ENDIF (SDF_SUPPORT)
+
+
+add_library(simu_loaders ${SIMU_LOADERS_SRCS})
--- a/c_tools/stacking/CMakeLists.txt
+++ b/c_tools/stacking/CMakeLists.txt
@ -0,0 +1,39 @@
+include_directories(${CMAKE_CURRENT_BINARY_DIR})
+
+SET(stackVoids_SRCS stackVoids.cpp)
+add_genopt(stackVoids_SRCS stackVoids.ggo stackVoids_conf STRUCTNAME stackVoids_info)
+add_executable(stackVoids ${stackVoids_SRCS})
+target_link_libraries(stackVoids  ${ZOB_LIBS})
+
+SET(stackVoidsZero_SRCS stackVoidsZero.cpp)
+add_genopt(stackVoidsZero_SRCS stackVoidsZero.ggo stackVoidsZero_conf STRUCTNAME stackVoidsZero_info)
+add_executable(stackVoidsZero ${stackVoidsZero_SRCS})
+target_link_libraries(stackVoidsZero ${ZOB_LIBS})
+
+set(computeVelocityProfile_SRCS computeVelocityProfile.cpp)
+add_genopt(computeVelocityProfile_SRCS computeVelocityProfile.ggo computeVelocityProfile_conf STRUCT Params)
+add_executable(computeVelocityProfile ${computeVelocityProfile_SRCS})
+target_link_libraries(computeVelocityProfile  ${ZOB_LIBS})
+
+
+set(stackDensityField_SRCS stackDensityField.cpp)
+add_genopt(stackDensityField_SRCS stackDensityField.ggo stackDensityField_conf STRUCT PARAMS)
+add_executable(stackDensityField ${stackDensityField_SRCS})
+target_link_libraries(stackDensityField ${ZOB_LIBS})
+
+
+
+set(stackVelocityField_SRCS stackVelocityField.cpp)
+add_genopt(stackVelocityField_SRCS stackVelocityField.ggo stackVelocityField_conf STRUCT PARAMS)
+add_executable(stackVelocityField ${stackVelocityField_SRCS})
+target_link_libraries(stackVelocityField ${ZOB_LIBS})
+
+SET(pruneVoids_SRCS pruneVoids.cpp)
+add_genopt(pruneVoids_SRCS pruneVoids.ggo pruneVoids_conf STRUCTNAME pruneVoids_info)
+add_executable(pruneVoids ${pruneVoids_SRCS})
+target_link_libraries(pruneVoids ${ZOB_LIBS})
+
+SET(makeAHFOutput_SRCS makeAHFOutput.cpp)
+add_genopt(makeAHFOutput_SRCS makeAHFOutput.ggo makeAHFOutput_conf STRUCTNAME makeAHFOutput_info)
+add_executable(makeAHFOutput ${makeAHFOutput_SRCS})
+target_link_libraries(makeAHFOutput ${ZOB_LIBS})
--- a/c_tools/zobov2/CMakeLists.txt
+++ b/c_tools/zobov2/CMakeLists.txt
@ -0,0 +1 @@
+subdirs(jozov2 voz1b1)
--- a/c_tools/zobov2/jozov2/CMakeLists.txt
+++ b/c_tools/zobov2/jozov2/CMakeLists.txt
@ -0,0 +1,24 @@
+function(omp_add_flags TARGET LANG)
+   if(OPENMP_FOUND)
+     if(NOT LANG)
+       get_target_property(LANG ${TARGET} LINKER_LANGUAGE)
+     endif()
+     if(LANG MATCHES "C(XX)?")
+       set_property(TARGET ${TARGET} APPEND
+                    PROPERTY COMPILE_FLAGS ${OpenMP_${LANG}_FLAGS})
+       set_property(TARGET ${TARGET} APPEND
+                    PROPERTY LINK_FLAGS ${OpenMP_${LANG}_FLAGS})
+     else()
+       message(WARNING "omp_add_flags: target '${TARGET}'"
+                      " link language '${LANG}' is not supported")
+    endif()
+  endif()
+endfunction()
+
+add_executable(jozov2 jozov2.cpp jozov2_io.cpp jozov2_zones.cpp jozov2_watershed.cpp findrtop.c)
+
+if (ENABLE_OPENMP)
+  Find_Package(OpenMP)
+  omp_add_flags(jozov2 CXX)
+  add_definitions(-DOPENMP)
+ENDIF(ENABLE_OPENMP)
--- a/c_tools/zobov2/voz1b1/CMakeLists.txt
+++ b/c_tools/zobov2/voz1b1/CMakeLists.txt
@ -0,0 +1,4 @@
+add_executable(voz1b1_2 voz1b1.cpp vozutil.c voz_io.cpp)
+target_link_libraries(voz1b1_2 ${QHULL_LIBRARY} ${COSMOTOOL_LIBRARY} ${MATH_LIB})
+
+include_directories(${COSMOTOOL_INCLUDE_PATH} ${QHULL_INCLUDE_PATH})
--- a/external/cosmotool/CMakeLists.txt
+++ b/external/cosmotool/CMakeLists.txt
@ -0,0 +1,86 @@
+cmake_minimum_required(VERSION 2.6)
+list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}")
+
+project(CosmoToolbox)
+
+include(GetGitRevisionDescription)
+include(ExternalProject)
+include(FindOpenMP)
+
+get_git_head_revision(HEAD GIT_VER)
+
+option(BUILD_SHARED_LIBS "Build shared libraries." OFF)
+option(BUILD_STATIC_LIBS "Build static libraries." ON)
+option(ENABLE_OPENMP "Enable OpenMP support." OFF)
+option(ENABLE_SHARP "Enable SPHT support." ON)
+
+find_path(NETCDF_INCLUDE_PATH NAMES netcdf.h)
+find_path(NETCDFCPP_INCLUDE_PATH NAMES netcdfcpp.h netcdf)
+find_path(GSL_INCLUDE_PATH NAMES gsl/gsl_blas.h)
+
+IF(EXISTS ${NETCDFCPP_INCLUDE_PATH}/netcdf)
+  SET(FOUND_NETCDF4 1)
+  FILE(WRITE ${CMAKE_BINARY_DIR}/src/ctool_netcdf_ver.hpp "#define NETCDFCPP4 1")
+ELSE(EXISTS ${NETCDFCPP_INCLUDE_PATH}/netcdf)
+  SET(FOUND_NETCDF3 1)
+  FILE(WRITE ${CMAKE_BINARY_DIR}/src/ctool_netcdf_ver.hpp "#undef NETCDFCPP4")
+ENDIF(EXISTS ${NETCDFCPP_INCLUDE_PATH}/netcdf)
+
+find_library(NETCDF_LIBRARY netcdf)
+find_library(NETCDFCPP_LIBRARY NAMES netcdf_c++ netcdf_c++4)
+find_library(GSL_LIBRARY gsl)
+find_library(GSLCBLAS_LIBRARY gslcblas)
+
+if (ENABLE_SHARP)
+  SET(SHARP_SOURCE ${CMAKE_SOURCE_DIR}/external/sharp)
+  SET(DEP_BUILD ${CMAKE_SOURCE_DIR}/external/sharp/auto)
+  ExternalProject_Add(sharp
+    SOURCE_DIR ${SHARP_SOURCE}
+    BUILD_IN_SOURCE 1 
+    CONFIGURE_COMMAND ${SHARP_SOURCE}/configure --prefix=${DEP_BUILD}
+    BUILD_COMMAND ${CMAKE_MAKE_PROGRAM}
+    INSTALL_COMMAND echo "No install"
+  )
+  SET(SHARP_LIBRARY ${DEP_BUILD}/lib/libsharp.a)
+  SET(SHARP_LIBRARIES ${SHARP_LIBRARY})
+  SET(SHARP_INCLUDE_PATH ${DEP_BUILD}/include)
+endif (ENABLE_SHARP)
+
+
+set(HDF5_FIND_COMPONENTS HL CXX)
+if(HDF5_ROOTDIR)
+  SET(ENV{HDF5_ROOT} ${HDF5_ROOTDIR})
+endif(HDF5_ROOTDIR)
+include(FindHDF5)
+
+include(FindPkgConfig)
+
+pkg_check_modules(FFTW3 fftw3>=3.3)
+pkg_check_modules(FFTW3F fftw3f>=3.3)
+pkg_check_modules(EIGEN3 eigen3)
+
+include(FindPackageHandleStandardArgs)
+set(NETCDF_FIND_REQUIRED TRUE)
+set(GSL_FIND_REQUIRED TRUE)
+FIND_PACKAGE_HANDLE_STANDARD_ARGS(NetCDF DEFAULT_MSG NETCDF_LIBRARY NETCDFCPP_LIBRARY NETCDF_INCLUDE_PATH)
+FIND_PACKAGE_HANDLE_STANDARD_ARGS(GSL DEFAULT_MSG GSL_LIBRARY GSLCBLAS_LIBRARY GSL_INCLUDE_PATH)
+
+
+set(GSL_LIBRARIES ${GSL_LIBRARY} ${GSLCBLAS_LIBRARY})
+
+# CPACK Configuration
+SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "A toolbox for impatient cosmologists")
+SET(CPACK_PACKAGE_VENDOR "Guilhem Lavaux")
+SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_CURRENT_SOURCE_DIR}/LICENCE_CeCILL_V2")
+SET(CPACK_PACKAGE_VERSION_MAJOR "1")
+SET(CPACK_PACKAGE_VERSION_MINOR "0")
+SET(CPACK_PACKAGE_VERSION_PATCH "0-${GIT_VER}")
+SET(CPACK_PACKAGE_INSTALL_DIRECTORY "CosmoToolbox-${GalaxExplorer_VERSION_MAJOR}.${GalaxExplorer_VERSION_MINOR}")
+SET(CPACK_STRIP_FILES "lib/libCosmoTool.so")
+SET(CPACK_SOURCE_IGNORE_FILES 
+"/CVS/;/\\\\.git/;/\\\\.svn/;\\\\.swp$;\\\\.#;/#;.*~;cscope.*;/CMakeFiles/;.*\\\\.cmake;Makefile")
+
+add_subdirectory(src)
+add_subdirectory(sample)
+
+include(CPack)
--- a/external/cosmotool/sample/CMakeLists.txt
+++ b/external/cosmotool/sample/CMakeLists.txt
@ -0,0 +1,65 @@
+SET(tolink ${GSL_LIBRARIES} CosmoTool ${CosmoTool_LIBS})
+include_directories(${CMAKE_SOURCE_DIR}/src ${FFTW3_INCLUDE_DIRS} ${EIGEN3_INCLUDE_DIRS} ${NETCDF_INCLUDE_PATH} ${GSL_INCLUDE_PATH})
+
+IF(SHARP_INCLUDE_PATH)
+  include_directories(BEFORE ${SHARP_INCLUDE_PATH})
+ENDIF(SHARP_INCLUDE_PATH)
+
+add_executable(testBQueue testBQueue.cpp)
+target_link_libraries(testBQueue ${tolink})
+
+add_executable(testInterpolate testInterpolate.cpp)
+target_link_libraries(testInterpolate ${tolink})
+
+add_executable(testSmooth testSmooth.cpp)
+target_link_libraries(testSmooth ${tolink})
+
+add_executable(testkd testkd.cpp)
+target_link_libraries(testkd ${tolink})
+
+add_executable(testkd2 testkd2.cpp)
+target_link_libraries(testkd2 ${tolink})
+
+add_executable(testkd3 testkd3.cpp)
+target_link_libraries(testkd3 ${tolink})
+
+add_executable(testDelaunay testDelaunay.cpp)
+target_link_libraries(testDelaunay ${tolink})
+
+add_executable(testNewton testNewton.cpp)
+target_link_libraries(testNewton ${tolink})
+
+add_executable(testPool testPool.cpp)
+target_link_libraries(testPool ${tolink})
+
+if (HDF5_FOUND)
+	  add_executable(testReadFlash testReadFlash.cpp)
+	  target_link_libraries(testReadFlash ${tolink})
+endif (HDF5_FOUND)
+
+
+add_executable(testEskow testEskow.cpp)
+target_link_libraries(testEskow ${tolink})
+
+add_executable(testAlgo testAlgo.cpp)
+target_link_libraries(testAlgo ${tolink})
+
+add_executable(testBSP testBSP.cpp)
+target_link_libraries(testBSP ${tolink})
+
+if (FFTW3_FOUND AND FFTW3F_FOUND AND EIGEN3_FOUND)
+  add_executable(test_fft_calls test_fft_calls.cpp)
+  target_link_libraries(test_fft_calls ${tolink} ${FFTW3_LIBRARIES} ${FFTW3F_LIBRARIES})
+endif (FFTW3_FOUND AND FFTW3F_FOUND AND  EIGEN3_FOUND)
+
+if (ENABLE_SHARP AND SHARP_LIBRARY AND SHARP_INCLUDE_PATH AND EIGEN3_FOUND)
+  include_directories(${SHARP_INCLUDE_PATH})
+  add_executable(test_healpix_calls test_healpix_calls.cpp)
+  target_link_libraries(test_healpix_calls ${tolink} ${SHARP_LIBRARIES})
+  set_target_properties(test_healpix_calls PROPERTIES COMPILE_FLAGS ${OpenMP_CXX_FLAGS} LINK_FLAGS ${OpenMP_CXX_FLAGS})
+  add_dependencies(test_healpix_calls sharp)
+endif (ENABLE_SHARP AND SHARP_LIBRARY AND SHARP_INCLUDE_PATH AND EIGEN3_FOUND)
+
+add_executable(test_cosmopower test_cosmopower.cpp)
+target_link_libraries(test_cosmopower ${tolink})
+
--- a/external/cosmotool/src/CMakeLists.txt
+++ b/external/cosmotool/src/CMakeLists.txt
@ -0,0 +1,92 @@
+SET(CosmoTool_SRCS
+	fortran.cpp
+	interpolate.cpp
+	load_data.cpp
+	loadGadget.cpp
+	loadRamses.cpp
+	octTree.cpp
+	powerSpectrum.cpp
+	miniargs.cpp
+	growthFactor.cpp
+	cosmopower.cpp
+)
+
+IF(FOUND_NETCDF3)
+	SET(CosmoTool_SRCS ${CosmoTool_SRCS} yorick_nc3.cpp)
+ELSE(FOUND_NETCDF3)
+IF(FOUND_NETCDF4)
+	SET(CosmoTool_SRCS ${CosmoTool_SRCS} yorick_nc4.cpp)
+ENDIF(FOUND_NETCDF4)
+ENDIF(FOUND_NETCDF3)
+
+
+if (HDF5_FOUND)
+  set(CosmoTool_SRCS ${CosmoTool_SRCS}
+    h5_readFlash.cpp
+    loadFlash.cpp
+    )
+else(HDF5_FOUND)
+  set(CosmoTool_SRCS ${CosmoTool_SRCS}
+    loadFlash_dummy.cpp
+  )
+endif (HDF5_FOUND)
+
+SET(CosmoTool_SRCS ${CosmoTool_SRCS}
+	bqueue.hpp
+	config.hpp
+	dinterpolate.hpp
+	field.hpp
+	fixArray.hpp
+	fortran.hpp
+	interpolate3d.hpp
+	interpolate.hpp
+	kdtree_leaf.hpp
+	load_data.hpp
+	loadGadget.hpp
+	loadRamses.hpp
+	loadSimu.hpp
+	miniargs.hpp
+	mykdtree.hpp
+	octTree.hpp
+	powerSpectrum.hpp
+	sparseGrid.hpp
+	sphSmooth.hpp
+	yorick.hpp
+	growthFactor.hpp
+)
+
+include_directories(${GSL_INCLUDE_PATH} ${NETCDF_INCLUDE_PATH} ${NETCDFCPP_INCLUDE_PATH} ${CMAKE_BINARY_DIR}/src)
+
+set(CosmoTool_LIBS  ${NETCDFCPP_LIBRARY} ${NETCDF_LIBRARY} ${GSL_LIBRARIES})
+if (HDF5_FOUND)
+  set(CosmoTool_LIBS ${CosmoTool_LIBS} ${HDF5_CXX_LIBRARIES} ${HDF5_LIBRARIES})
+  include_directories(${HDF5_INCLUDE_DIRS})
+endif (HDF5_FOUND)
+
+set(CosmoTool_LIBS ${CosmoTool_LIBS} PARENT_SCOPE)
+
+if (BUILD_SHARED_LIBS)
+  add_library(CosmoTool SHARED ${CosmoTool_SRCS})
+  target_link_libraries(CosmoTool ${CosmoTool_LIBS})
+
+  if (BUILD_STATIC_LIBS)
+     add_library(CosmoTool_static STATIC ${CosmoTool_SRCS})
+  endif(BUILD_STATIC_LIBS)
+else (BUILD_SHARED_LIBS)
+  add_library(CosmoTool STATIC ${CosmoTool_SRCS})
+endif (BUILD_SHARED_LIBS)
+
+install(TARGETS CosmoTool 
+	LIBRARY DESTINATION lib
+	ARCHIVE DESTINATION lib)
+
+if (BUILD_SHARED_LIBS)
+  install(TARGETS CosmoTool_static 
+  	  LIBRARY DESTINATION lib
+	  ARCHIVE DESTINATION lib)
+endif (BUILD_SHARED_LIBS)
+
+install(DIRECTORY . DESTINATION include/CosmoTool
+	FILES_MATCHING PATTERN "*.hpp")
+install(DIRECTORY . DESTINATION include/CosmoTool
+	FILES_MATCHING PATTERN "*.tcc")
--- a/pipeline/datasets/example_observation.py
+++ b/pipeline/datasets/example_observation.py
@ -0,0 +1,250 @@
+#+
+#   VIDE -- Void IDentification and Examination -- ./pipeline/sdss/sdss_dr7LCDM.py
+#   Copyright (C) 2010-2013 Guilhem Lavaux
+#   Copyright (C) 2011-2013 P. M. Sutter
+#
+#   This program is free software; you can redistribute it and/or modify
+#   it under the terms of the GNU General Public License as published by
+#   the Free Software Foundation; version 2 of the License.
+# 
+#
+#   This program is distributed in the hope that it will be useful,
+#   but WITHOUT ANY WARRANTY; without even the implied warranty of
+#   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#   GNU General Public License for more details.
+#
+#   You should have received a copy of the GNU General Public License along
+#   with this program; if not, write to the Free Software Foundation, Inc.,
+#   51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+#+
+#!/usr/bin/env python
+
+# does analysis in real space assuming LCDM cosmology
+
+import os
+import numpy as np
+from void_python_tools.backend.classes import *
+
+# does full void analysis. Also generates 2d/1d stacked plots and hubble diagram
+
+# to combine multiple samples:
+#   For example, combining dim from 0.0-0.1 and bright from 0.1-0.2:
+#     1) add dim+bright to sampleList - "+" is required to detect combo!
+
+# if True, will scan log files for last known completed state and run from there
+continueRun = False
+
+# stages:
+#   1 : extract redshift slices from data
+#   2 : void extraction using zobov
+#   3 : removal of small voids and voids near the edge 
+#   4 : void stacking and combining
+#   5 : 1-d and 2-d profile generation
+#   6 : fitting and plotting stacked voids
+#   7 : determination of error bars (if requested)
+#   8 : hubble diagram generation
+#   9 : liklihood determination
+startCatalogStage = 1
+endCatalogStage   = 1
+
+catalogName = "lcdm"
+
+# where main data files are present/will go
+workDir      = os.getenv("HOME")+"/workspace/Voids/sdss_dr7LCDM/"
+inputDataDir = os.getenv("HOME")+"/workspace/Voids/catalogs/nyuvagc/"
+
+logDir = os.getenv("PWD")+"/../logs/sdss_dr7LCDM"
+figDir = os.getenv("PWD")+"/../figs/sdss_dr7LCDM"
+
+ZOBOV_PATH = os.getenv("PWD")+"/../zobov/"
+CTOOLS_PATH = os.getenv("PWD")+"/../c_tools/"
+
+freshStack = True # "no" to continue building onto existing stacked voids
+
+errorBars = "CALCULATED" # "ESTIMATED" for error bars from multiple null tests
+#errorBars = "ESTIMATED" # "ESTIMATED" for error bars from multiple null tests
+                        # "CALCULATED" to use fitting procedure 
+numIncoherentRuns = 100
+
+ranSeed = 101010
+
+useComoving = True # if true, convert to real space using LCDM cosmology
+
+# try different portions of data. available options: "all, central, edge"
+dataPortions = ["central", "all"]
+
+numZobovDivisions = 2
+numZobovThreads = 2
+
+dataSampleList = []
+
+
+newSample = Sample(fullName = "lss.dr72dim1.dat",
+                   nickName = "dim1",
+                   dataType = "observation",
+                   maskFile = inputDataDir+"/healpix/rast_window_512.fits",
+                   selFunFile = inputDataDir+"/czselfunc.all.dr72dim1.dat",
+                   zBoundary = (0.0, 0.05),
+                   zRange = (0.0, 0.05),
+                   skyFraction = 0.19,
+                   minVoidRadius = 3.479,
+                   fakeDensity = 0.01,
+                   volumeLimited = True,
+                   includeInHubble = False,
+                   partOfCombo = True,
+                   isCombo = False,
+                   comboList= None)
+newSample.addStack(0.0, 0.1, 8, 12, False, True)
+newSample.addStack(0.0, 0.1, 12, 16, False, True)
+newSample.addStack(0.0, 0.1, 16, 20, False, True)
+newSample.addStack(0.0, 0.1, 20, 28, False, True)
+dataSampleList.append(newSample)
+
+newSample = Sample(fullName = "lss.dr72dim2.dat",
+                   nickName = "dim2",
+                   dataType = "observation",
+                   maskFile = inputDataDir+"/healpix/rast_window_512.fits",
+                   selFunFile = inputDataDir+"/czselfunc.all.dr72dim2.dat",
+                   zBoundary = (0.0, 0.1),
+                   zRange = (0.05, 0.1),
+                   skyFraction = 0.19,
+                   minVoidRadius = 4.723,
+                   fakeDensity = 0.01,
+                   volumeLimited = True,
+                   includeInHubble = False,
+                   partOfCombo = True,
+                   isCombo = False,
+                   comboList= None)
+newSample.addStack(0.0, 0.1, 8, 12, False, True)
+newSample.addStack(0.0, 0.1, 12, 16, False, True)
+newSample.addStack(0.0, 0.1, 16, 20, False, True)
+newSample.addStack(0.0, 0.1, 20, 28, False, True)
+dataSampleList.append(newSample)
+
+newSample = Sample(fullName = "lss.dr72dim1+dim2.dat",
+                   nickName = "dim1+dim2",
+                   dataType = "observation",
+                   maskFile = inputDataDir+"/healpix/rast_window_512.fits",
+                   selFunFile = inputDataDir+"/czselfunc.all.dr72dim.dat",
+                   zBoundary = (0.0, 0.1),
+                   zRange = (0.0, 0.1),
+                   skyFraction = 0.19,
+                   minVoidRadius = 4.723,
+                   fakeDensity = 0.01,
+                   profileBinSize = "auto",
+                   volumeLimited = True,
+                   includeInHubble = True,
+                   partOfCombo = False,
+                   isCombo = True,
+                   comboList= ("lss.dr72dim1.dat", "lss.dr72dim2.dat"))
+newSample.addStack(0.0, 0.1, 8, 12, True, False)
+newSample.addStack(0.0, 0.1, 12, 16, True, False)
+newSample.addStack(0.0, 0.1, 16, 20, True, False)
+newSample.addStack(0.0, 0.1, 20, 28, True, False)
+dataSampleList.append(newSample)
+
+
+newSample = Sample(fullName = "lss.dr72bright1.dat",
+                   nickName = "bright1",
+                   dataType = "observation",
+                   maskFile = inputDataDir+"/healpix/rast_window_512.fits",
+                   selFunFile = inputDataDir+"/czselfunc.all.dr72bright1.dat",
+                   zBoundary = (0.0, 0.15),
+                   zRange = (0.1, 0.15),
+                   skyFraction = 0.19,
+                   minVoidRadius = 6.763,
+                   fakeDensity = 0.01,
+                   volumeLimited = True,
+                   includeInHubble = False,
+                   partOfCombo = True,
+                   isCombo = False,
+                   comboList= None)
+newSample.addStack(0.1, 0.2, 13, 20, False, True)
+newSample.addStack(0.1, 0.2, 20, 28, False, True)
+newSample.addStack(0.1, 0.2, 28, 36, False, True)
+newSample.addStack(0.1, 0.2, 36, 44, False, True)
+dataSampleList.append(newSample)
+
+newSample = Sample(fullName = "lss.dr72bright2.dat",
+                   nickName = "bright2",
+                   dataType = "observation",
+                   maskFile = inputDataDir+"/healpix/rast_window_512.fits",
+                   selFunFile = inputDataDir+"/czselfunc.all.dr72bright2.dat",
+                   zBoundary = (0.0, 0.2),
+                   zRange = (0.15, 0.2),
+                   skyFraction = 0.19,
+                   minVoidRadius = 10.844,
+                   fakeDensity = 0.001,
+                   volumeLimited = True,
+                   includeInHubble = False,
+                   partOfCombo = True,
+                   isCombo = False,
+                   comboList= None)
+newSample.addStack(0.1, 0.2, 13, 20, False, True)
+newSample.addStack(0.1, 0.2, 20, 28, False, True)
+newSample.addStack(0.1, 0.2, 28, 36, False, True)
+newSample.addStack(0.1, 0.2, 36, 44, False, True)
+dataSampleList.append(newSample)
+
+newSample = Sample(fullName = "lss.dr72bright1+bright2.dat",
+                   nickName = "bright1+bright2",
+                   dataType = "observation",
+                   maskFile = inputDataDir+"/healpix/rast_window_512.fits",
+                   zBoundary = (0.0, 0.2),
+                   zRange = (0.1, 0.2),
+                   skyFraction = 0.19,
+                   minVoidRadius = -1,
+                   fakeDensity = -1,
+                   profileBinSize = "auto",
+                   volumeLimited = True,
+                   includeInHubble = True,
+                   partOfCombo = False,
+                   isCombo = True,
+                   comboList= ("lss.dr72bright1.dat", "lss.dr72bright2.dat"))
+newSample.addStack(0.1, 0.2, 13, 20, True, False)
+newSample.addStack(0.1, 0.2, 20, 28, True, False)
+newSample.addStack(0.1, 0.2, 28, 36, True, False)
+newSample.addStack(0.1, 0.2, 36, 44, True, False)
+dataSampleList.append(newSample)
+
+newSample = Sample(fullName = "lss.dr72lrgdim.dat",
+                   nickName = "lrgdim",
+                   dataType = "observation",
+                   maskFile = inputDataDir+"/healpix/rast_window_512.fits",
+                   selFunFile = inputDataDir+"/czselfunc.all.dr72lrgdim.dat",
+                   zBoundary = (0.16, 0.36),
+                   zRange = (0.16, 0.36),
+                   skyFraction = 0.19,
+                   minVoidRadius = 24,
+                   fakeDensity = 0.001, 
+                   profileBinSize = 2, # KEEP
+                   volumeLimited = True,
+                   includeInHubble = True,
+                   partOfCombo = False,
+                   isCombo = False,
+                   comboList= None)
+newSample.addStack(0.16, 0.36, 54, 70, True, False, zMinPlot=0.2)
+newSample.addStack(0.16, 0.36, 70, 106, True, False, zMinPlot=0.2)
+dataSampleList.append(newSample)
+
+newSample = Sample(fullName = "lss.dr72lrgbright.dat",
+                   nickName = "lrgbright",
+                   dataType = "observation",
+                   maskFile = inputDataDir+"/healpix/rast_window_512.fits",
+                   selFunFile = inputDataDir+"/czselfunc.all.dr72lrgbright.dat",
+                   zBoundary = (0.36, 0.44),
+                   zRange = (0.36, 0.44),
+                   skyFraction = 0.19,
+                   minVoidRadius = 38,
+                   fakeDensity = 0.001,
+                   profileBinSize = "auto",
+                   volumeLimited = True,
+                   includeInHubble = False,
+                   partOfCombo = False,
+                   isCombo = False,
+                   comboList= None)
+newSample.addStack(0.36, 0.44, 76, 92, False, False)
+newSample.addStack(0.36, 0.44, 92, 108, False, False)
+dataSampleList.append(newSample)
+
+
--- a/pipeline/datasets/example_simulation.py
+++ b/pipeline/datasets/example_simulation.py
@ -0,0 +1,144 @@
+#+
+#   VIDE -- Void IDEntification pipeline -- ./pipeline/datasets/mergertree.py
+#   Copyright (C) 2010-2013 Guilhem Lavaux
+#   Copyright (C) 2011-2013 P. M. Sutter
+#
+#   This program is free software; you can redistribute it and/or modify
+#   it under the terms of the GNU General Public License as published by
+#   the Free Software Foundation; version 2 of the License.
+# 
+#
+#   This program is distributed in the hope that it will be useful,
+#   but WITHOUT ANY WARRANTY; without even the implied warranty of
+#   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#   GNU General Public License for more details.
+#
+#   You should have received a copy of the GNU General Public License along
+#   with this program; if not, write to the Free Software Foundation, Inc.,
+#   51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+#+
+import os
+
+# -----------------------------------------------------------------------------
+# -----------------------------------------------------------------------------
+# CONFIGURATION
+
+startCatalogStage = 0
+endCatalogStage = 0
+continueRun = False
+
+startAPStage = 1
+endAPStage = 2
+
+# directory for the input simulation/observational particle files
+catalogDir = os.getenv("HOME")+"/workspace/Voids/catalogs/mergertree1024/"
+
+# path to HOD code
+hodPath = os.getenv("HOME")+"/projects/Voids/hod/HOD.x"
+
+# where to put the final void catalog, figures, and output logs
+voidOutputDir = os.getenv("HOME")+"/workspace/Voids/mergertree1024/"
+figDir = os.getenv("PWD")+"/../figs/mergertree1024/"
+logDir = os.getenv("PWD")+"/../logs/mergertree1024/"
+
+# where to place the pipeline scripts
+scriptDir = os.getenv("PWD")+"/mergertree1024/"
+
+# simulation or observation?
+dataType = "simulation"
+
+# available formats for simulation: gadget, mergertree
+dataFormat = "sdf"
+dataUnit = 1 # as multiple of Mpc/h
+
+# place particles on the lightcone?
+useLightCone = False
+
+# also do peculiar velocities?
+doPecVel = False
+
+# common filename of particle files
+particleFileBase = "mf_4s_1G_1k_NNNNN"
+particleFileDummy = 'NNNNN'
+
+# list of file numbers for the particle files
+# to get particle file name, we take particleFileBase+fileNum
+fileNums = ["1.000"]
+
+# redshift of each file in the above list
+redshifts = ["0.0"]
+
+# how many independent slices along the z-axis?
+numSlices = 1
+#numSlices = 4
+numAPSlices = 1
+
+# how many subdivisions along the x- and y- axis?
+#   ( = 2 will make 4 subvolumes for each slice, = 3 will make 9, etc.)
+numSubvolumes = 1
+
+# prefix to give all outputs
+prefix = "mt_"
+
+# list of desired subsamples - these are in unts of h Mpc^-3!
+subSamples = [0.1, 0.05, 0.02, 0.01, 0.004, 0.002, 0.001, 0.0003, 0.0001]
+#doSubSampling = False # do the subsampling in preparation script?
+doSubSampling = True # do the subsampling in preparation script?
+
+# common filename of halo files, leave blank to ignore halos
+haloFileBase = "mf_4s_1G_1k_bgc2_NNNNN.sdf"
+haloFileDummy = 'NNNNN'
+
+# minimum halo mass cuts to apply for the halo catalog
+#   use "none" to get all halos
+minHaloMasses = ["none", 1.2e13]
+#minHaloMasses = [7.0e11, 1.2e13]
+
+# locations of data in the halo catalog
+haloFileMCol  = 6
+haloFileXCol  = 0
+haloFileYCol  = 1
+haloFileZCol  = 2
+haloFileVXCol = 3
+haloFileVYCol = 4
+haloFileVZCol = 5
+haloFileColSep = ','
+haloFileNumComLines = 0
+
+# adjust these two parameters given the memory contraints on your system:
+#   numZobovDivisions: how many sub-volumes per dimension will zobov process
+#   numZobovThreads: how many sub-volumes to process at once?   
+numZobovDivisions = 4
+numZobovThreads = 4
+
+# simulation information
+numPart = 1024*1024*1024
+lbox = 999.983 # Mpc/h
+omegaM = 0.2847979853038958
+hubble = 0.6962
+
+#galDens = 0.000225
+hodParmList = [
+  {'name'       : "LowRes", #BOSS: Manera et al. 2012, eq. 26
+   'Mmin'       : 0.0,
+   'M1'         : 1.e14,
+   'sigma_logM' : 0.596,
+   'alpha'      : 1.0127,
+   'Mcut'       : 1.19399e13,
+   'galDens'    : 0.0002,
+  },
+
+  {'name'       : "HighRes",
+   'Mmin'       : 0.0,
+   #'Mmin'       : 1.99525e12,
+   'M1'         : 3.80189e13,
+   'sigma_logM' : 0.21,
+   'alpha'      : 1.12,
+   'Mcut'       : 6.91831e11,
+   'galDens'    : 0.02,
+  }
+]
+
+# END CONFIGURATION
+# -----------------------------------------------------------------------------
+# -----------------------------------------------------------------------------
--- a/python_tools/void_python_tools/apTools/chi2/init.py
+++ b/python_tools/void_python_tools/apTools/chi2/init.py
@ -17,6 +17,4 @@
 #   with this program; if not, write to the Free Software Foundation, Inc.,
 #   51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
 #+
-from velocityProfileFitNative import *
-from likelihood import * 
 from cosmologyTools import *
--- a/python_tools/void_python_tools/apTools/chi2/cosmologyTools.py
+++ b/python_tools/void_python_tools/apTools/chi2/cosmologyTools.py
@ -24,7 +24,7 @@ import numpy as np
 import scipy.integrate as integrate
 from void_python_tools.backend import *

-__all__=['expansion', 'angularDiameter', 'expectedStretch', 'aveStretch', 'aveExpansion', 'aveStretchCone', 'aveWeightedStretch']
+__all__=['expansion', 'angularDiameter', 'aveExpansion']

 # returns 1/E(z) for the given cosmology
 def expansion(z, Om = 0.27, Ot = 1.0, w0 = -1.0, wa = 0.0):
@ -42,113 +42,6 @@ def angularDiameter(z, Om = 0.27, Ot = 1.0, w0 = -1.0, wa = 0.0):
  da = integrate.quad(expansion, 0.0, z, args=(Om, Ot, w0, wa))[0]
  return da
  
-  
-# returns expected void stretch for the given cosmology
-def expectedStretch(z, Om = 0.27, Ot = 1.0, w0 = -1.0, wa = 0.0):
-  ez = 1./expansion(z, Om=Om, Ot=Ot, w0=w0, wa=wa)
-  da = angularDiameter(z, Om=Om, Ot=Ot, w0=w0, wa=wa)
-  return ez*da/z
-
-# -----------------------------------------------------------------------------
-# returns average expected void stretch for a given redshift range 
-#   assuming a cone 
-def aveStretchCone(zStart, zEnd, skyFrac = 0.19, Om = 0.27, Ot = 1.0, 
-                   w0 = -1.0, wa = 0.0):
-  #print "assuming observation!", skyFrac
-  if zStart == 0.0: zStart = 1.e-6
-
-  h1 = zStart 
-  h2 = zEnd
-
-  r1 = skyFrac * 4* np.pi * zStart**2
-  r2 = skyFrac * 4 * np.pi * zEnd**2
-
-  # surface area of a slice within a cone
-  def coneSlice(x, h, r):
-    return np.pi * (r/h*x)**2
-
-  def coneFunc(z, h, r, Om = 0.27, Ot = 1.0, w0 = -1.0, wa = 0.0):
-    return coneSlice(z, h, r) * expectedStretch(z, Om, Ot, w0, wa)
-
-  aveHigh = integrate.quad(coneFunc, 0.0, zEnd, args=(h2, r2, Om, Ot, w0, wa), full_output=1)[0]
-  aveLow = integrate.quad(coneFunc, 0.0, zStart, args=(h1, r1, Om, Ot, w0, wa), full_output=1)[0]
-  volumeHigh = integrate.quad(coneSlice, 0.0, zEnd, args=(h2, r2))[0]
-  volumeLow = integrate.quad(coneSlice, 0.0, zStart, args=(h1, r1))[0]
-
-  return (aveHigh-aveLow)/(volumeHigh-volumeLow)
-
-# returns average expected void stretch for a given redshift range
-def aveStretch(sample, zStart, zEnd, 
-               Om = 0.27, Ot = 1.0, w0 = -1.0, wa = 0.0):
-  if zStart == 0.0: zStart = 1.e-6
-
-  if sample.dataType == "observation":
-    stretch =  aveStretchCone(zStart, zEnd, 
-                          skyFrac=sample.skyFraction, Om=Om, Ot=Ot, 
-                          w0=w0, wa=wa)
-  else:
-    ave = integrate.quad(expectedStretch, zStart, zEnd, 
-                         args=(Om, Ot, w0, wa))[0]
-    ave /= (zEnd-zStart)
-    stretch = ave
-
-  # if in comoving space, calculate stretch for fiducial cosmology
-  # and take relative amount
-  if not sample.useLightCone or sample.useComoving:
-    if sample.dataType == "observation":
-      stretchFid =  aveStretchCone(zStart, zEnd, 
-                          skyFrac=sample.skyFraction, Om=sample.omegaM, Ot=Ot, 
-                          w0=w0, wa=wa)
-    else:
-      ave = integrate.quad(expectedStretch, zStart, zEnd, 
-                           args=(sample.omegaM, Ot, w0, wa))[0]
-      ave /= (zEnd-zStart)
-      stretchFid = ave
-
-  stretch = stretchFid/stretch
-
-  return stretch
-
-
-# -----------------------------------------------------------------------------
-# returns average expected void stretch for a given redshift range 
-#   weighted by an actual void distribution
-def aveWeightedStretch(zStart, zEnd, skyFrac = 0.19, Om = 0.27, Ot = 1.0, 
-                   w0 = -1.0, wa = 0.0, dist=None, bins=None, 
-                   useComoving=True, OmFid=None):
-  if zStart == 0.0: zStart = 1.e-6
-
-  def weightedSlice(x):
-    return np.interp(x, bins[:-1], dist)
- 
-  def weightedFunc(z, Om = 0.27, Ot = 1.0, w0 = -1.0, wa = 0.0):
-    return expectedStretch(z, Om, Ot, w0, wa) *\
-           weightedSlice(z) 
-
-  ave = integrate.quad(weightedFunc, zStart, zEnd, args=(Om, Ot, w0, wa),
-                       full_output=1)[0]
-  volume = integrate.quad(weightedSlice, zStart, zEnd, full_output=1)[0]
-
-  if volume == 0.0: volume = 1.0 
-  stretch = ave/volume
- 
-  # if in comoving space, calculate stretch for fiducial cosmology
-  # and take relative amount
-  if useComoving:
-    ave = integrate.quad(weightedFunc, zStart, zEnd, args=(OmFid, 
-                         Ot, w0, wa),
-                         full_output=1)[0]
-    volume = integrate.quad(weightedSlice, zStart, zEnd, full_output=1)[0]
-  
-    if volume == 0.0: volume = 1.0 
-    stretchFid = ave/volume
-
-  if stretchFid != 0.0: 
-    stretch = stretchFid/stretch
-
-  return stretch
-
-
 # -----------------------------------------------------------------------------
 # returns average expected expansion for a given redshift range
 def aveExpansion(zStart, zEnd, Om = 0.27, Ot = 1.0, w0 = -1.0, wa = 0.0):
--- a/python_tools/void_python_tools/apTools/profiles/init.py
+++ b/python_tools/void_python_tools/apTools/profiles/init.py
@ -17,10 +17,4 @@
 #   with this program; if not, write to the Free Software Foundation, Inc.,
 #   51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
 #+
-from build import *
-from draw import *
-from fit import *
-from inertia import *
-from mcmc import *
-from generateExpFigure import *
 from getSurveyProps import *
--- a/python_tools/void_python_tools/backend/init.py
+++ b/python_tools/void_python_tools/backend/init.py
@ -19,4 +19,3 @@
 #+
 from classes import *
 from launchers import *
-from catalogPrep import *
--- a/python_tools/void_python_tools/backend/launchers.py
+++ b/python_tools/void_python_tools/backend/launchers.py
--- a/python_tools/void_python_tools/partUtil/partUtil.py
+++ b/python_tools/void_python_tools/partUtil/partUtil.py
@ -34,7 +34,7 @@ ncFloat = 'f8'

 # -----------------------------------------------------------------------------
 def loadPart(sampleDir):
-    #print "    Loading particle data..."
+    print "    Loading particle data..."
    sys.stdout.flush()

    with open(sampleDir+"/sample_info.dat", 'rb') as input:
--- a/python_tools/void_python_tools/xcor/xcorlib.py
+++ b/python_tools/void_python_tools/xcor/xcorlib.py
@ -2,72 +2,12 @@ import numpy as np

 def cic( x, Lbox, Lboxcut = 0, Nmesh = 128, weights = None ):

- if weights == None: weights = 1
- wm = np.mean(weights)
- ws = np.mean(weights**2)
-
- d = np.mod(x/(Lbox+2*Lboxcut)*Nmesh,1)
-
- box = ([Lboxcut,Lbox+Lboxcut],[Lboxcut,Lbox+Lboxcut],[Lboxcut,Lbox+Lboxcut])
-
- rho = np.histogramdd(x, range = box, bins = Nmesh, weights = weights*(1-d[:,0])*(1-d[:,1])*(1-d[:,2]))[0] \
-     + np.roll(np.histogramdd(x, range = box, bins = Nmesh, weights = weights*d[:,0]*(1-d[:,1])*(1-d[:,2]))[0],1,0) \
-     + np.roll(np.histogramdd(x, range = box, bins = Nmesh, weights = weights*(1-d[:,0])*d[:,1]*(1-d[:,2]))[0],1,1) \
-     + np.roll(np.histogramdd(x, range = box, bins = Nmesh, weights = weights*(1-d[:,0])*(1-d[:,1])*d[:,2])[0],1,2) \
-     + np.roll(np.roll(np.histogramdd(x, range = box, bins = Nmesh, weights = weights*d[:,0]*d[:,1]*(1-d[:,2]))[0],1,0),1,1) \
-     + np.roll(np.roll(np.histogramdd(x, range = box, bins = Nmesh, weights = weights*d[:,0]*(1-d[:,1])*d[:,2])[0],1,0),1,2) \
-     + np.roll(np.roll(np.histogramdd(x, range = box, bins = Nmesh, weights = weights*(1-d[:,0])*d[:,1]*d[:,2])[0],1,1),1,2) \
-     + np.roll(np.roll(np.roll(np.histogramdd(x, range = box, bins = Nmesh, weights = weights*d[:,0]*d[:,1]*d[:,2])[0],1,0),1,1),1,2)
-
- rho /= wm
- 
- rho = rho/rho.mean() - 1.
- 
- return (rho, wm, ws)
- 
+  return 

 def powcor( d1, d2, Lbox, Nmesh = 128, Nbin = 100, scale = 'lin', cor = False ):

- # Fourier transform
- d1 = np.fft.fftn(d1)
- d2 = np.fft.fftn(d2)
-
- # CIC correction
- wid = np.indices(np.shape(d1)) - Nmesh/2
- #wid[np.where(wid >= Nmesh/2)] -= Nmesh
- wid = wid*np.pi/Nmesh + 1e-100
- wcic = np.prod(np.sin(wid)/wid,0)**2
-
- # Shell average power spectrum
- dk = 2*np.pi/Lbox
- Pk = np.conj(d1)*d2*(Lbox/Nmesh**2)**3
- Pk = np.fft.fftshift(Pk)/wcic**2
-
- (Nm, km, Pkm, SPkm) = shellavg(np.real(Pk), dk, Nmesh, Nbin = Nbin, xmin = 0., xmax = Nmesh*dk/2, scale = scale)
- 
- # Inverse Fourier transform and shell average correlation function
- if cor == True:
-  dx = Lbox/Nmesh
-  Xr = np.fft.ifftshift(np.fft.ifftn(np.fft.ifftshift(Pk)))*(Nmesh/Lbox)**3
-
-  (Nmx, rm, Xrm, SXrm) = shellavg(np.real(Xr), dx, Nmesh, Nbin = Nbin, xmin = dx, xmax = 140., scale = scale)
-  
-  return ((Nm, km, Pkm, SPkm),(Nmx, rm, Xrm, SXrm))
- 
- else: return (Nm, km, Pkm, SPkm)
-
+  return
 
 def shellavg( f, dx, Nmesh, Nbin = 100, xmin = 0., xmax = 1., scale = 'lin' ):

- x = np.indices(np.shape(f)) - Nmesh/2
- #x[np.where(x >= Nmesh/2)] -= Nmesh
- x = dx*np.sqrt(np.sum(x**2,0))
- if scale == 'lin': bins = xmin+(xmax-xmin)* (np.arange(Nbin+1)/float(Nbin))
- if scale == 'log': bins = xmin*(xmax/xmin)**(np.arange(Nbin+1)/float(Nbin))
-
- Nm = np.histogram(x, bins = bins)[0]
- xm = np.histogram(x, bins = bins, weights = x)[0]/Nm
- fm = np.histogram(x, bins = bins, weights = f)[0]/Nm
- fs = np.sqrt((np.histogram(x, bins = bins, weights = f**2)[0]/Nm - fm**2)/(Nm-1))
- 
- return (Nm, xm, fm, fs)
+  return 
--- a/zobov/CMakeLists.txt
+++ b/zobov/CMakeLists.txt
@ -0,0 +1,16 @@
+
+add_executable(voz1b1 voz1b1.c readfiles.c vozutil.c voz.h)
+target_link_libraries(voz1b1 ${QHULL_LIBRARY} ${MATH_LIB})
+
+
+add_executable(jozov jozov.c findrtop.c)
+target_link_libraries(jozov ${MATH_LIB})
+
+add_executable(vozinit vozinit.c readfiles.c)
+target_link_libraries(vozinit ${MATH_LIB})
+
+
+add_executable(voztie voztie.c readfiles.c)
+target_link_libraries(voztie ${MATH_LIB})
+
+