re-added some essential routines; updated example sceipts to reflect new layout

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  stacking)
+subdirs(libzobov mock pruning jozov2)

c_tools/libzobov/pruneVoids.ggo

@@ -1,44 +0,0 @@
-package "removeEdgeVoids"
-version "alpha"
-
-
-option "configFile" - "Configuration filename" string optional
-
-option "partFile" - "Particle file from generateFromCatalog" string required
-
-option "extraInfo" - "Extra particle file from generateFromCatalog" string required
-
-option "voidDesc" - "Void list from ZOBOV" string required
-
-option "void2Zone" - "Zone file from ZOBOV" string required
-
-option "partVol" - "Particle volume file from ZOBOV" string required
-
-option "partAdj" - "Adjacency file from ZOBOV" string required
-
-option "zone2Part" - "Particle file from ZOBOV" string required
-option "mockIndex" - "Beginning index of mock particles" int required
-
-option "numVoids" - "Number of voids" int required
-
-option "isObservation" - "We are working with observational data" flag off
-
-option "useComoving" - "Void positions are in comoving coordinates" flag off
-
-option "omegaM" - "Omega_M for redshift convertion" double optional default="0.27"
-
-option "zMin" - "Minimum redshift of sample" double optional default="0.0"
-option "zMax" - "Maximum redshift of sample" double optional default="10.0"
-
-option "rMin" - "Minimum allowable void radius" double optional default="0.0"
-
-option "outputDir" - "Directory to place outputs" string required
-option "sampleName" - "unique string to assign to outputs" string required
-
-option "periodic" - "Set of edges which are periodic" string optional default="xy"
-
-option "tolerance" - "Fraction of void width to consider edge" double optional default="1.0"
-
-option "centralRadFrac" - "Fraction of void radii to consider central region" double optional default="4"
-
-option "maxCentralDen" - "Maximum central density to accept as a void" double optional default="0.2" 

c_tools/stacking/CMakeLists.txt

@@ -1,41 +0,0 @@
-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})
-
-install(TARGETS pruneVoids DESTINATION ${VIDE_BIN})

examples/example_observation/example_observation.py

@@ -34,13 +34,14 @@ startCatalogStage = 1
 endCatalogStage   = 3
 
 basePath = os.path.dirname(os.path.abspath(__file__))
-basePath = os.path.abspath(os.path.join(basePath,"..","..","..","examples"))
+#basePath = os.path.abspath(os.path.join(basePath,"..","..","..","examples"))
 
 # directory for input data files
 inputDataDir = basePath
 
 # void catalog output directory
-workDir = os.path.join(basePath,"example_observation")
+workDir = basePath
+#workDir = os.path.join(basePath,"example_observation")
 
 # output directory for log files
 logDir = os.path.join(basePath,"logs","example_observation")

examples/example_simulation/example_simulation.py

@@ -36,10 +36,10 @@ startCatalogStage = 1
 endCatalogStage   = 3
 
 # directory for the input simulation files
-catalogDir = PWD+"/examples/"
+catalogDir = PWD
 
 # void catalog output directory
-voidOutputDir = PWD+"/examples/example_simulation/"
+voidOutputDir = PWD+"/outputs/"
 
 # output directory for log files
 logDir = PWD+"/logs/example_simulation/"

python_tools/setup.py

@@ -31,6 +31,5 @@ setup(
 #    cmdclass = {'build_ext': build_ext},
     include_dirs = [np.get_include()],
     packages=
-       ['vide','vide.backend','vide.voidUtil',
+       ['vide','vide.backend','vide.voidUtil'],
-        'vide.apTools.profiles','vide.apTools.chi2',],
 )

python_tools/vide/backend/__init__.py

@@ -19,3 +19,4 @@
 #+
 from .classes import *
 from .launchers import *
+from .cosmologyTools import *

python_tools/vide/backend/launchers.py

@@ -20,7 +20,7 @@
 # -----------------------------------------------------------------------------
 # -----------------------------------------------------------------------------
 # routines which communicate with individual data analysis portions -
-#   they make the analyzeVoids.py script easier to read
+#   they make the main script easier to read
 
 import os
 import glob
@@ -35,6 +35,7 @@ import sys
 from   pylab import figure
 from   netCDF4 import Dataset
 from vide.backend.classes import *
+from vide.backend.cosmologyTools import *
 import pickle
 import vide.apTools as vp
 import scipy.interpolate as interpolate

python_tools/vide/voidUtil/plotUtil.py

@@ -24,7 +24,7 @@ from .plotDefs import *
 import numpy as np
 import os
 import pylab as plt
-import vide.apTools as vp
+import vide.backend.cosmologyTools as vp
 from vide.voidUtil import getArray, shiftPart, getVoidPart
 
 def fill_between(x, y1, y2=0, ax=None, **kwargs):

python_tools/void_pipeline/__main__.py

@@ -32,7 +32,7 @@ import pickle
 # ------------------------------------------------------------------------------
 
 if (len(sys.argv) == 1):
-  print("Usage: ./generateCatalog.py parameter_file.py")
+  print("Usage: python3 -m void_pipeline parameter_file.py")
   exit(-1)
 
 if (len(sys.argv) > 1):