prepareCatalogs now first loads a parameter file full of defaults

python_tools/pipeline_source/defaults.py

@@ -0,0 +1,132 @@
+#+
+#   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
+
+# -----------------------------------------------------------------------------
+# -----------------------------------------------------------------------------
+# DEFAULT CONFIGURATION
+
+startCatalogStage = 1
+endCatalogStage = 3
+
+startAPStage = 1
+endAPStage = 5
+
+continueRun = True
+dataPortions = ["central"]
+
+# directory for the input simulation/observational particle files
+catalogDir = os.getenv("HOME")+"/workspace/Voids/catalog/"
+
+# 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//"
+figDir = os.getenv("PWD")+"/../figs/"
+logDir = os.getenv("PWD")+"/../logs/"
+
+# where to place the pipeline scripts
+scriptDir = os.getenv("PWD")+"/scripts//"
+
+# 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_512_NNNNN"
+particleFileDummy = 'NNNNN'
+
+# list of file numbers for the particle files
+# to get particle file name, we take particleFileBase+fileNum
+fileNums = ["0.667", "0.500"]
+
+# redshift of each file in the above list
+redshifts = ["0.5", "1.0"]
+
+# how many independent slices along the z-axis?
+numSlices = 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 = [1.0]
+doSubSampling = True # do the subsampling in preparation script?
+
+# common filename of halo files, leave blank to ignore halos
+haloFileBase = "mf_4s_1G_512_bgc2_NNNNN.sdf"
+haloFileDummy = 'NNNNN'
+
+# minimum halo mass cuts to apply for the halo catalog
+#   use "none" to get all halos
+minHaloMasses = [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 = 2
+numZobovThreads = 2
+
+# simulation information
+numPart = 512*512*512
+lbox = 999.983 # Mpc/h
+omegaM = 0.2847979853038958
+hubble = 0.6962
+
+#galDens = 0.000225
+hodParmList = [
+  {'name'       : "dr9mid", #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,
+  },
+]
+
+# END CONFIGURATION
+# -----------------------------------------------------------------------------
+# -----------------------------------------------------------------------------

python_tools/pipeline_source/prepareCatalogs.in.py

@@ -56,6 +56,10 @@ parser.add_argument('--parm', dest='parm',
 args = parser.parse_args()
 
 
+defaultsFile = "@CMAKE_BINARY_DIR@/python_tools/pipeline_source/defaults.py"
+parms = imp.load_source("name", defaultsFile)
+globals().update(vars(parms))
+
 filename = args.parm
 print " Loading parameters from", filename
 if not os.access(filename, os.F_OK):
@@ -109,16 +113,16 @@ def writeScript(setName, dataFileNameBase, dataFormat,
   scriptFileName = scriptDir + "/" + setName + ".py"
   scriptFile = open(scriptFileName, 'w')
 
-  scriptFile.write("""#!/usr/bin/env/python
+  header = """#!/usr/bin/env/python
 import os
 from void_python_tools.backend.classes import *
 
-continueRun = False # set to True to enable restarting aborted jobs
+continueRun = {continueRun} # set to True to enable restarting aborted jobs
-startCatalogStage = 1
+startCatalogStage = {startCatalogStage}
-endCatalogStage   = 3
+endCatalogStage   = {endCatalogStage}
                
-startAPStage = 1
+startAPStage = {startAPStage}
-endAPStage = 1
+endAPStage = {endAPStage}
 
 regenerateFlag = False
 ZOBOV_PATH = "@CMAKE_BINARY_DIR@/zobov/"
@@ -130,10 +134,16 @@ ranSeed = 101010
 useLCDM = False
 bias = 1.16
 
-dataPortions = ["central"]
+dataPortions = {dataPortions}
 dataSampleList = []
-""")
+           """
 
+  scriptFile.write(header.format(startCatalogStage=startCatalogStage,
+                                 endCatalogStage=endCatalogStage,
+                                 startAPStage=startAPStage,
+                                 endAPStage=endAPStage,
+                                 continueRun=continueRun,
+                                 dataPortions=dataPortions))
 
   dataInfo = """
 setName = "{setName}"
@@ -175,6 +185,8 @@ newSample = Sample(dataFile = "{dataFile}",
                    useLightCone = {useLightCone},
                    subsample = "{subsample}")
 dataSampleList.append(newSample)
+newSample.addStack(0.0, 5.0, 10, 15, False, False)
+newSample.addStack(0.0, 5.0, 15, 20, False, False)
 newSample.addStack(0.0, 5.0, 20, 25, False, False)
 newSample.addStack(0.0, 5.0, 30, 35, False, False)
 newSample.addStack(0.0, 5.0, 40, 45, False, False)
@@ -693,6 +705,8 @@ if (args.hod or args.all) and haloFileBase != "":
       outFileName = catalogDir+"/"+sampleName+".dat"
       os.system("mv %s/hod.mock %s" % (catalogDir, outFileName))
       os.system("rm %s/hod.*" % catalogDir)
+      os.system("rm ./hod.par")
+      os.system("rm ./hod-usedvalues")
 
     if dataFormat == "sdf": os.system("rm %s" % haloFile)