Merged in python3 (pull request #5)

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

python_tools/vide/backend/classes.py

@@ -0,0 +1,225 @@
+#+
+#   VIDE -- Void IDentification and Examination -- ./python_tools/vide/backend/classes.py
+#   Copyright (C) 2010-2014 Guilhem Lavaux
+#   Copyright (C) 2011-2014 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.
+#+
+# classes and routines used to support scripts
+
+import os
+from numpy import abs
+import matplotlib as mpl
+mpl.use('Agg')
+
+LIGHT_SPEED = 299792.458
+
+class Stack:
+  zMin = 0.0
+  zMax = 0.1
+  rMin = 5
+  rMax = 15
+  zMinPlot = 0.0
+  zMaxPlot = 0.1
+  includeInHubble = True
+  partOfCombo = False
+  needProfile = True
+  rescaleMode = "rmax" # options: "rmax" to scale to largest void in stack
+                       #          "rv"   normalize each void
+  maxVoids = -1 # maximum number of voids to allow in the stack
+
+  def __init__(self, zMin, zMax, rMin, rMax, includeInHubble, partOfCombo, 
+               zMinPlot=None, needProfile=True, rescaleMode="rmax",
+               maxVoids=-1, fittingMode="mcmc"):
+    self.zMin = zMin
+    self.zMax = zMax
+    self.rMin = rMin
+    self.rMax = rMax
+    self.zMaxPlot = zMax
+    self.includeInHubble = includeInHubble
+    self.partOfCombo = partOfCombo
+    self.needProfile = needProfile
+    self.rescaleMode = rescaleMode
+    self.maxVoids = maxVoids
+    self.fittingMode = fittingMode
+   
+    if zMinPlot == None:
+      self.zMinPlot = self.zMin
+    else:
+      self.zMinPlot = zMinPlot
+
+class Sample:
+  dataType = "observation"
+  dataFormat = "sdss"
+  dataFile = "lss.dr72dim.dat"
+  dataUnit = 1
+  fullName = "lss.dr72dim.dat"
+  nickName = "dim"
+  zobovDir = ""
+  maskFile = "rast_window_512.fits"
+  selFunFile = "czselfunc.all.dr72dim.dat"
+  zBoundary = (0.0, 0.1)
+  zBoundaryMpc = (0., 300)
+  shiftSimZ = False
+  zRange    = (0.0, 0.1)
+  omegaM    = 0.27
+  minVoidRadius = -1
+  fakeDensity = 0.01
+  profileBinSize = 2 # Mpc
+  autoNumInStack = -1 # set to >0 to automatically generate stacks of size N
+  autoPartInStack = -1 # set to >0 to automatically generate stacks with N particles
+  numAPSlices = 1
+  volumeLimited = True
+  includeInHubble = True
+  partOfCombo  = False
+  isCombo = False
+  
+  comboList = []
+
+  # applies to simulations only
+  boxLen = 1024 # Mpc/h
+  usePecVel = False
+  subsample = 1.0
+  numSubvolumes = 1
+  mySubvolume = 1
+
+  stacks = []
+
+  def __init__(self, dataFile="", fullName="", dataUnit=1,
+               nickName="", maskFile="", selFunFile="",
+               zBoundary=(), zRange=(), zBoundaryMpc=(), shiftSimZ=False,
+               minVoidRadius=-1, fakeDensity=0.01, volumeLimited=True,
+               numAPSlices=1,
+               includeInHubble=True, partOfCombo=False, isCombo=False, 
+               comboList=(), profileBinSize=2.0,
+               boxLen=1024, usePecVel=False, omegaM=0.27, 
+               numSubvolumes=1, mySubvolume=1, dataFormat="sdss",
+               useComoving=True,
+               dataType="observation",
+               subsample=1.0, useLightCone=False, autoNumInStack=-1,
+               autoPartInStack=-1):
+    self.dataFile = dataFile
+    self.fullName = fullName
+    self.nickName = nickName
+    self.maskFile = maskFile
+    self.selFunFile = selFunFile
+    self.zBoundary = zBoundary 
+    self.zBoundaryMpc = zBoundaryMpc
+    self.shiftSimZ = shiftSimZ
+    self.zRange = zRange
+    self.minVoidRadius = minVoidRadius
+    self.fakeDensity = fakeDensity
+    self.volumeLimited = volumeLimited
+    self.includeInHubble = includeInHubble 
+    self.partOfCombo = partOfCombo 
+    self.isCombo = isCombo
+    self.comboList = comboList
+    self.numAPSlices = numAPSlices
+    self.zobovDir = None
+    self.profileBinSize = profileBinSize
+    self.dataType = dataType
+    self.boxLen = boxLen
+    self.usePecVel = usePecVel
+    self.omegaM = omegaM
+    self.numSubvolumes = numSubvolumes
+    self.mySubvolume = mySubvolume
+    self.dataFormat = dataFormat
+    self.subsample = subsample
+    self.useLightCone = useLightCone
+    self.dataUnit = dataUnit
+    self.useComoving = useComoving
+    self.autoNumInStack = autoNumInStack
+    self.autoPartInStack = autoPartInStack
+
+    self.stacks = []
+
+  def addStack(self, zMin, zMax, rMin, rMax, 
+                includeInHubble, partOfCombo,zMinPlot=None, 
+                needProfile=True, rescaleMode="rmax",
+                maxVoids=-1, fittingMode="mcmc"):
+    self.stacks.append(Stack(zMin, zMax, rMin, rMax,
+                            includeInHubble, partOfCombo, 
+                            zMinPlot=zMinPlot, needProfile=needProfile,
+                            rescaleMode=rescaleMode,
+                            maxVoids=maxVoids,
+                            fittingMode=fittingMode))
+
+  def getHubbleStacks(self):
+    stacksForHubble = []
+    for stack in self.stacks:
+      if stack.includeInHubble:
+        stacksForHubble.append(stack)
+    return stacksForHubble
+
+  def getUniqueRBins(self):
+    uniqueRStacks = []
+    for stack in self.stacks:
+      if not stack.includeInHubble:
+        continue
+      alreadyHere = False
+      for stackCheck in uniqueRStacks:
+        if stack.rMin == stackCheck.rMin and stack.rMax == stackCheck.rMax:
+          alreadyHere = True
+          break
+      if not alreadyHere:
+        uniqueRStacks.append(stack)
+    return uniqueRStacks
+
+  def getUniqueZBins(self):
+    uniqueZStacks = []
+    for stack in self.stacks:
+      if not stack.includeInHubble:
+        continue
+      alreadyHere = False
+      for stackCheck in uniqueZStacks:
+        if stack.zMin == stackCheck.zMin and stack.zMax == stackCheck.zMax:
+          alreadyHere = True
+          break
+      if not alreadyHere:
+        uniqueZStacks.append(stack)
+    return uniqueZStacks
+
+# -----------------------------------------------------------------------------
+# -----------------------------------------------------------------------------
+def jobSuccessful(logFile, doneString):
+  jobDone = False
+  checkLine = ""
+  if os.access(logFile, os.F_OK):
+    #filelines = file(logFile, "r").readlines()
+    #if len(filelines) >= 1:
+    #  checkLine = filelines[-1]
+    for line in open(logFile, 'r'):
+      if doneString in line: jobDone = True
+  return jobDone
+
+def getStackSuffix(zMin, zMax, rMin, rMax, dataPortion, customLine=""):
+  return "z"+str(zMin)+"-"+str(zMax)+"_"+str(rMin)+"-"+str(rMax)+\
+           "Mpc"+customLine+"_"+dataPortion
+
+def getPeriodic(sample):
+  periodicLine = ""
+  if sample.dataType != "observation":
+    if sample.numSubvolumes == 1: periodicLine += "xy"
+    if abs(sample.zBoundaryMpc[1]  - sample.zBoundaryMpc[0] - \
+              sample.boxLen) <= 1.e-1:
+      periodicLine += "z"
+  return periodicLine
+
+def my_import(name):
+    mod = __import__(name)
+    components = name.split('.')
+    for comp in components[1:]:
+        mod = getattr(mod, comp)
+    return mod