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Merged in python3 (pull request #5)

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Port to python3, large code cleanup

* Fixed command line for cosmotool

* Fix path

* Dump command line is log file

* Fix important typo

* Modify paths for example

* Fix path again

* Use an explicit constructor

* Change file to open (python 2->3)

* python3 fix for xrange in periodic_kdtree.py

* Fixed index for Np, numPart, numZones, numZonesTot, partID, zoneID in catalogUtil.py
This commit is contained in:
Guilhem Lavaux 2020-12-29 08:56:33 +00:00
parent 8249256508
commit affb56ff48
392 changed files with 4092 additions and 260938 deletions
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71
python_tools/pipeline_source/prepareInputs.in.py
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@ -1,6 +1,6 @@
#!/usr/bin/env python
#+
# VIDE -- Void IDentification and Examination -- ./python_tools/pipeline_source/prepareCatalogs.in.py
# VIDE -- Void IDentification and Examination -- ./python_tools/pipeline_source/prepareInputs.in.py
# Copyright (C) 2010-2014 Guilhem Lavaux
# Copyright (C) 2011-2014 P. M. Sutter
#
@ -18,12 +18,11 @@
# with this program; if not, write to the Free Software Foundation, Inc.,
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
#+
#+
import numpy as np
import os
import sys
import void_python_tools as vp
import vide as vp
import argparse
import imp
import subprocess
@ -59,9 +58,9 @@ parms = imp.load_source("name", defaultsFile)
globals().update(vars(parms))
filename = args.parm
print " Loading parameters from", filename
print(" Loading parameters from", filename)
if not os.access(filename, os.F_OK):
print " Cannot find parameter file %s!" % filename
print(" Cannot find parameter file %s!" % filename)
exit(-1)
parms = imp.load_source("name", filename)
globals().update(vars(parms))
@ -163,7 +162,7 @@ def writeScript(setName, dataFileNameBase, dataFormat,
header = """#!/usr/bin/env/python
import os
from void_python_tools.backend.classes import *
from vide.backend.classes import *
continueRun = {continueRun} # set to True to enable restarting aborted jobs
startCatalogStage = {startCatalogStage}
@ -235,13 +234,13 @@ dataSampleList.append(newSample)
# converter from redshift to comoving distance
zVsDY = np.linspace(0., zBox+8*lbox*100./LIGHT_SPEED, 10000)
zVsDX = np.zeros(len(zVsDY))
for i in xrange(len(zVsDY)):
for i in range(len(zVsDY)):
zVsDX[i] = vp.angularDiameter(zVsDY[i], Om=Om)
boxWidthZ = np.interp(vp.angularDiameter(zBox,Om=Om)+100. / \
LIGHT_SPEED*lbox, zVsDX, zVsDY)-zBox
for iSlice in xrange(numSlices):
for iSlice in range(numSlices):
if useLightCone:
dzSafe = 0.03
@ -277,8 +276,8 @@ dataSampleList.append(newSample)
else:
dataFileName = dataFileNameBase + fileNum + suffix
for iX in xrange(numSubvolumes):
for iY in xrange(numSubvolumes):
for iX in range(numSubvolumes):
for iY in range(numSubvolumes):
mySubvolume = "%d%d" % (iX, iY)
@ -322,7 +321,7 @@ if not os.access(catalogDir, os.F_OK): os.mkdir(catalogDir)
baseResolution = float(numPart)/lbox/lbox/lbox # particles/Mpc^3
prevSubSample = -1
subSamples = sorted(subSamples, reverse=True)
for iSubSample in xrange(len(subSamples)):
for iSubSample in range(len(subSamples)):
subSampleList = subSamples[0:iSubSample+1]
@ -333,7 +332,7 @@ for iSubSample in xrange(len(subSamples)):
elif subSampleMode == 'relative':
keepFractionList.append(float(subSample))
else:
print "Unrecognized subSampleMode = ", subSampleMode
print("Unrecognized subSampleMode = ", subSampleMode)
exit(-1)
thisSubSample = subSamples[iSubSample]
maxKeep = keepFractionList[-1] * numPart
@ -348,7 +347,7 @@ for iSubSample in xrange(len(subSamples)):
fileNums[iRedshift]))
if args.script or args.all:
print " Doing subsample", thisSubSample, "scripts"
print(" Doing subsample", thisSubSample, "scripts")
sys.stdout.flush()
setName = prefix+"ss"+str(thisSubSample)
@ -397,11 +396,11 @@ for iSubSample in xrange(len(subSamples)):
if (args.subsample or args.all) and doSubSamplingInPrep:
print " Doing subsample", thisSubSample
print(" Doing subsample", thisSubSample)
sys.stdout.flush()
for (iRedshift, redshift) in enumerate(redshifts):
print " redshift", redshift
print(" redshift", redshift)
sys.stdout.flush()
if dataFormat == "multidark" or dataFormat == "sdf":
@ -500,7 +499,7 @@ for iSubSample in xrange(len(subSamples)):
outFile.write("%s\n" %(redshift))
outFile.write("%d\n" %(maxKeep))
for i in xrange(int(maxKeep)):
for i in range(int(maxKeep)):
x = np.random.uniform()*lbox
y = np.random.uniform()*lbox
z = np.random.uniform()*lbox
@ -517,7 +516,7 @@ for iSubSample in xrange(len(subSamples)):
if (args.script or args.all) and haloFileBase != "":
for minHaloMass in minHaloMasses:
print " Doing halo script", minHaloMass
print(" Doing halo script", minHaloMass)
sys.stdout.flush()
# estimate number of halos to get density
@ -580,15 +579,15 @@ if (args.script or args.all) and haloFileBase != "":
dataFileNameList = fileList)
if (args.halos or args.all) and haloFileBase != "" and len(minHaloMasses) > 0:
print " Doing halos - mass"
print(" Doing halos - mass")
sys.stdout.flush()
for minHaloMass in minHaloMasses:
print " min halo mass = ", minHaloMass
print(" min halo mass = ", minHaloMass)
sys.stdout.flush()
for (iRedshift, redshift) in enumerate(redshifts):
print " z = ", redshift
print(" z = ", redshift)
sys.stdout.flush()
if haloFileDummy == '':
@ -671,7 +670,7 @@ if (args.halos or args.all) and haloFileBase != "" and len(minHaloMasses) > 0:
if (args.script or args.all) and haloFileBase != "":
for haloDen in haloDenList:
print " Doing halo script", haloDen
print(" Doing halo script", haloDen)
sys.stdout.flush()
# estimate number of halos to get density
@ -710,15 +709,15 @@ if (args.script or args.all) and haloFileBase != "":
dataFileNameList = fileList)
if (args.halos or args.all) and haloFileBase != "":
print " Doing halos - density"
print(" Doing halos - density")
sys.stdout.flush()
for haloDen in haloDenList:
print " halo density = ", haloDen
print(" halo density = ", haloDen)
sys.stdout.flush()
for (iRedshift, redshift) in enumerate(redshifts):
print " z = ", redshift
print(" z = ", redshift)
sys.stdout.flush()
if haloFileDummy == '':
@ -746,7 +745,7 @@ if (args.halos or args.all) and haloFileBase != "":
numPartExpect = int(np.ceil(haloDen * lbox**3))
if numPart < numPartExpect:
print " ERROR: not enough halos to support that density! Maximum is %g" % (1.*numPart / lbox**3)
print(" ERROR: not enough halos to support that density! Maximum is %g" % (1.*numPart / lbox**3))
exit(-1)
@ -779,7 +778,7 @@ if (args.halos or args.all) and haloFileBase != "":
actualDen = 1.*numPart / lbox**3
keepFraction = haloDen / actualDen
if numPart < numPartExpect:
print " ERROR: not enough galaxies to support that density! Maximum is %g" % (1.*numPart / lbox**3)
print(" ERROR: not enough galaxies to support that density! Maximum is %g" % (1.*numPart / lbox**3))
exit(-1)
numKept = 0
@ -861,7 +860,7 @@ root_filename {workDir}/hod_{sampleName}
"""
if (args.script or args.all) and haloFileBase != "":
print " Doing HOD scripts"
print(" Doing HOD scripts")
sys.stdout.flush()
for thisHod in hodParmList:
@ -871,7 +870,7 @@ if (args.script or args.all) and haloFileBase != "":
outFileName = sampleName+".dat"
fileList.append(outFileName)
print " ", thisHod['name']
print(" ", thisHod['name'])
# estimate number of halos to get density
numPart = thisHod['galDensFinal'] * lbox**3
@ -893,10 +892,10 @@ if (args.script or args.all) and haloFileBase != "":
dataFileNameList = fileList)
if (args.hod or args.all) and haloFileBase != "":
print " Doing HOD"
print(" Doing HOD")
sys.stdout.flush()
for (iRedshift, redshift) in enumerate(redshifts):
print " z = ", redshift
print(" z = ", redshift)
sys.stdout.flush()
if haloFileDummy == '':
@ -918,7 +917,7 @@ if (args.hod or args.all) and haloFileBase != "":
haloFile = outFile
for thisHod in hodParmList:
print " ", thisHod['name']
print(" ", thisHod['name'])
sys.stdout.flush()
sampleName = getSampleName(prefix+"hod_"+thisHod['name'], redshift, False)
@ -955,16 +954,16 @@ if (args.hod or args.all) and haloFileBase != "":
hodWorked = False
for line in open(tempFile):
if "MLO" in line:
print " (minimum halo mass = ", line.split()[1], ")"
print(" (minimum halo mass = ", line.split()[1], ")")
hodWorked = True
break
if hodWorked:
os.unlink(tempFile)
else:
print "HOD Failed! Log follows:"
print("HOD Failed! Log follows:")
for line in open(tempFile):
print line
print(line)
exit(-1)
# now randomly subsample the galaxies to get desired density
@ -977,7 +976,7 @@ if (args.hod or args.all) and haloFileBase != "":
inFile.close()
if numPartActual < numPartExpect:
print " ERROR: not enough galaxies to support that density! Maximum is %g" % (1.*numPartActual / lbox**3)
print(" ERROR: not enough galaxies to support that density! Maximum is %g" % (1.*numPartActual / lbox**3))
exit(-1)
actualDen = 1.*numPartActual / lbox**3
@ -1015,4 +1014,4 @@ if (args.hod or args.all) and haloFileBase != "":
if dataFormat == "sdf": os.system("rm %s" % haloFile)
print " Done!"
print(" Done!")