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/apTools/chi2/__init__.py

@@ -0,0 +1,20 @@
+#+
+#   VIDE -- Void IDentification and Examination -- ./python_tools/vide/apTools/chi2/__init__.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.
+#+
+from .cosmologyTools import *

python_tools/vide/apTools/chi2/cosmologyTools.py

@@ -0,0 +1,53 @@
+#+
+#   VIDE -- Void IDentification and Examination -- ./python_tools/vide/apTools/chi2/cosmologyTools.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.
+#+
+# a suite of functions to compute expansion rates, angular diameter 
+# distances, and expected void stretching
+
+import numpy as np
+import scipy.integrate as integrate
+from vide.backend import *
+
+__all__=['expansion', 'angularDiameter', 'aveExpansion']
+
+# returns 1/E(z) for the given cosmology
+def expansion(z, Om = 0.27, Ot = 1.0, w0 = -1.0, wa = 0.0):
+  ez = Om * (1+z)**3 + (Ot-Om)# * (1+z)**(3.+3*wz)
+  #ez = Om * (1+z)**3 + (Ot-Om)# * integrade.quad(eosDE, 0.0, z, args=(w0,wa))[0]
+  ez = 1./np.sqrt(ez)
+  return ez
+
+# returns DE value at redshift z
+def eosDE(z, w0 = -1.0, wa = 0.0):
+  return w0 + wa*z/(1+z)
+  
+# returns D_A(z) for the given cosmology
+def angularDiameter(z, Om = 0.27, Ot = 1.0, w0 = -1.0, wa = 0.0):
+  da = integrate.quad(expansion, 0.0, z, args=(Om, Ot, w0, wa))[0]
+  return da
+  
+# -----------------------------------------------------------------------------
+# returns average expected expansion for a given redshift range
+def aveExpansion(zStart, zEnd, Om = 0.27, Ot = 1.0, w0 = -1.0, wa = 0.0):
+  if zStart == 0.0: zStart = 1.e-6
+  ave = integrate.quad(expansion, zStart, zEnd, args=(Om, Ot, w0, wa))[0]
+  ave = (zEnd-zStart)/ave
+  return ave
+
+