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

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This commit is contained in:
Paul M. Sutter 2024-05-22 15:13:15 -04:00
parent 45f22a2c29
commit 541223fd07
11 changed files with 12 additions and 1308 deletions
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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})
#target_link_libraries(computeAverageDistortion ${ZOB_LIBS})
subdirs(libzobov mock stacking)
subdirs(libzobov mock pruning jozov2)

1213
c_tools/libzobov/pruneVoids.cpp
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File diff suppressed because it is too large Load diff

44
c_tools/libzobov/pruneVoids.ggo
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@ -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"

41
c_tools/stacking/CMakeLists.txt
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@ -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})

5
examples/example_observation/example_observation.py
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@ -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")

4
examples/example_simulation/example_simulation.py
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@ -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/"

3
python_tools/setup.py
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@ -31,6 +31,5 @@ setup(
# cmdclass = {'build_ext': build_ext},
include_dirs = [np.get_include()],
packages=
['vide','vide.backend','vide.voidUtil',
'vide.apTools.profiles','vide.apTools.chi2',],
['vide','vide.backend','vide.voidUtil'],
)

1
python_tools/vide/backend/__init__.py
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@ -19,3 +19,4 @@
#+
from .classes import *
from .launchers import *
from .cosmologyTools import *

3
python_tools/vide/backend/launchers.py
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@ -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

2
python_tools/vide/voidUtil/plotUtil.py
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@ -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):

2
python_tools/void_pipeline/__main__.py
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@ -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):