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added README and cleaned up prepareGadgetCatalog script

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P.M. Sutter 2012-11-01 08:39:21 -05:00
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README Normal file
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After compiling, go to the pipeline directory.
Edit the parameters at the top of prepareGadgetCatalog.py: decide where to put outputs, how many redshifts to do, how many slices, subdivisions, subsamples, etc. etc.
Note that eventually prepareGadgetCatalog will be replaced by the more general and flexible prepareCatalogs.
prepareGadgetCatalogs will produce a pipeline script for each subsampling you choose. If you have multiple redshift particle files, and choose multiple slices and/or subdivisions, they will be packaged in the same pipeline script.
Run "./generateCatalog.py [name of pipeline script]" for each script written by prepareGadgetCatalog. This will run generateMock, zobov, and pruneVoids. At the end of it, you should have a void catalog for each redshift, slice, and subdivision.
Check the logfiles for any error messages.
See the README of the public void catalog for the format of the outputs.
I'm also working on incorporating plotting into the pipeline script, so that you can immediately get some basic info about the voids.
Please do not change the outputs of pruneVoids etc. without discussion, since further analysis relies on the current formats.
If you're wondering why these scripts are rather complex, it's because it can also support A-P analysis, which is much more complicated :)
We can talk about ways to incorporate your analysis into the pipline and to have your tools under this umbrella.
Good luck!

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pipeline/prepareGadgetCatalog.py
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#!/usr/bin/env python
# prepares input catalogs based on multidark simulations
# (borrows heavily from generateMock, but doesn't hold much in memory)
# also creates necessary analyzeVoids input files
# script which prepares inputs for gadget-based void run
import numpy as np
import os
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import void_python_tools as vp
import argparse
catalogDir = os.getenv("HOME")+"/workspace/Voids/catalogs/multidark/"
hodPath = os.getenv("HOME")+"/projects/Voids/hod/HOD.x"
# -----------------------------------------------------------------------------
# -----------------------------------------------------------------------------
# CONFIGURATION
voidOutputDir = os.getenv("HOME")+"/workspace/Voids/multidark/"
scriptDir = os.getenv("HOME")+"/projects/Voids/scripts/multidark/"
figDir = os.getenv("HOME")+"/projects/Voids/figs/multidark/"
logDir = os.getenv("HOME")+"/projects/Voids/logs/multidark/"
# directory for the input simulation/observational particle files
catalogDir = os.getenv("HOME")+"/workspace/Voids/catalogs/gadget/"
# where to put the final void catalog, figures, and output logs
voidOutputDir = os.getenv("HOME")+"/workspace/Voids/gadget/"
figDir = os.getenv("PWD")+"/../figs/gadget/"
logDir = os.getenv("PWD")+"/../logs/gadget/"
# where to place the pipeline scripts
scriptDir = os.getenv("PWD")+"/gadget/"
# simulation or observation?
dataType = "simulation"
# available formats for simulation: gadget, multidark
dataFormat = "gadget"
useLightCone = False # place particles on a light cone?
redshiftFileBase = "mdr1_particles_z" # common filename of particle files
redshifts = (("0.0", "0.53", "1.0")) # list of redshift particle files
# place particles on the lightcone?
useLightCone = False
numSlices = 4 # how many slices along the z-axis?
numSubvolumes = 1 # how many subdivisions along the x- and y-axes?
# common filename of particle files
redshiftFileBase = "mdr1_particles_z"
prefix = "testrun_" # prefix to give all outputs
subSamples = [ 0.01 ] # list of desired subsamples
# list of redshifts for the particle files
# to get particle file name, we take redshiftFileBase+redshift
redshifts = (("0.0", "0.53", "1.0"))
numPart = 1024*1024*1024 # number of particles in base catalog
# how many independent slices along the z-axis?
numSlices = 4
# 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 = "gadget_"
# list of desired subsamples
subSamples = [ 1.0, 0.1 ]
# simulation information
numPart = 1024*1024*1024
lbox = 1000 # Mpc/h
omegaM = 0.27
hubble = 0.70
# END CONFIGURATION
# -----------------------------------------------------------------------------
# -----------------------------------------------------------------------------
LIGHT_SPEED = 299792.458
#------------------------------------------------------------------------------
LIGHT_SPEED = 299792.458
def getSampleName(setName, redshift, useVel, iSlice=-1, iVol=-1):
sampleName = setName