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/profiles/getSurveyProps.py

@@ -0,0 +1,86 @@
+#+
+#   VIDE -- Void IDentification and Examination -- ./python_tools/vide/apTools/profiles/getSurveyProps.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.
+#+
+import numpy as np
+import healpy as healpy
+import scipy.integrate
+import vide as ct
+import os
+
+__all__=['getSurveyProps']
+   
+# returns the volume and galaxy density for a given redshit slice
+def getSurveyProps(maskFile, zmin, zmax, selFunMin, selFunMax, portion, selectionFuncFile=None, useComoving=False):
+
+  LIGHT_SPEED = 299792.458
+
+  mask = healpy.read_map(maskFile)
+  area = (1.*np.size(np.where(mask > 0)) / np.size(mask)) * 4.*np.pi
+
+  if useComoving:
+    zmin = LIGHT_SPEED/100.*ct.angularDiameter(zmin, Om=0.27)
+    zmax = LIGHT_SPEED/100.*ct.angularDiameter(zmax, Om=0.27)
+    selFunMin = LIGHT_SPEED/100.*ct.angularDiameter(selFunMin, Om=0.27)
+    selFunMax = LIGHT_SPEED/100.*ct.angularDiameter(selFunMax, Om=0.27)
+  else:
+    zmin = zmin * 3000
+    zmax = zmax * 3000
+    selFunMin *= 3000
+    selFunMax *= 3000
+  volume = area * (zmax**3  - zmin**3) / 3
+
+  if selectionFuncFile == None:
+    nbar = 1.0
+
+  elif not os.access(selectionFuncFile, os.F_OK):
+    print("   Warning, selection function file %s not found, using default of uniform selection." % selectionFuncFile)
+    nbar = 1.0
+
+  else:
+    selfunc = np.genfromtxt(selectionFuncFile)
+    selfunc = np.array(selfunc)
+    selfunc[:,0] = selfunc[:,0]/100.
+    selfuncUnity = selfunc
+    selfuncUnity[:,1] = 1.0
+    selfuncMin = selfunc[0,0]
+    selfuncMax = selfunc[-1,0]
+    selfuncDx = selfunc[1,0] - selfunc[0,0]
+    selfuncN = np.size(selfunc[:,0])
+  
+    selFunMin = max(selFunMin, selfuncMin)
+    selFunMax = min(selFunMax, selfuncMax)
+  
+  
+    def f(z): return selfunc[np.ceil((z-selfuncMin)/selfuncDx), 1]*z**2 
+    def fTotal(z): return selfuncUnity[np.ceil((z-selfuncMin)/selfuncDx), 1]*z**2 
+  
+    zrange = np.linspace(selFunMin, selFunMax)
+  
+    nbar = scipy.integrate.quad(f, selFunMin, selFunMax)
+    nbar = nbar[0]
+  
+    ntotal = scipy.integrate.quad(fTotal, 0.0, max(selfuncUnity[:,0]))
+    ntotal = ntotal[0]
+  
+    nbar = ntotal / area / nbar
+
+
+  #print "PROPERTIES: ", volume, nbar
+ 
+  return (volume, nbar)