Merge branch 'master' of https://bitbucket.org/cosmicvoids/vide_public

README

@@ -33,4 +33,9 @@ ccmake ./
 make
 cd pipeline/
 ./prepareInputs.py --scripts path/to/dataset.py
-./generateCatalog.py path/to/parameter_file.py
+./generateCatalog.py path/to/parameter_file.py
+
+Version Summary
+-----------------
+
+v1.0 - Initial Release

python_tools/void_python_tools/backend/launchers.py

@@ -37,6 +37,7 @@ from   netCDF4 import Dataset
 from void_python_tools.backend.classes import *
 import pickle
 import void_python_tools.apTools as vp
+import scipy.interpolate
 
 NetCDFFile = Dataset
 ncFloat = 'f8' # Double precision
@@ -265,6 +266,7 @@ def launchGenerate(sample, binPath, workDir=None, inputDataDir=None,
     zMax = sample.zBoundaryMpc[1]
 
     boxVol = (xMax-xMin)*(yMax-yMin)*(zMax-zMin)
+    nbar = 1.0
 
   numTracers = int(open(zobovDir+"/mask_index.txt", "r").read())
   numTotal = int(open(zobovDir+"/total_particles.txt", "r").read())
@@ -343,17 +345,75 @@ def launchZobov(sample, binPath, zobovDir=None, logDir=None, continueRun=None,
     subprocess.call(cmd, stdout=log, stderr=log)
     log.close()
 
-    # TODO re-weight the volumes based on selection function
-    #volFile = zobovDir+"/vol_"+sampleName+".dat"
-    #File = file(volFile)
-    #chk = np.fromfile(File, dtype=np.int32,count=1)
-    #vols = np.fromfile(File, dtype=np.float32,count=numPartTot)
+    # re-weight the volumes based on selection function
+    if sample.dataType == "observation" and \
+       sample.selFunFile != None:
+
+      # load volumes
+      volFile = zobovDir+"/vol_"+sampleName+".dat"
+      File = file(volFile)
+      numPartTot = np.fromfile(File, dtype=np.int32,count=1)
+      vols = np.fromfile(File, dtype=np.float32,count=numPartTot)
+      File.close()
+
+      # load redshifts
+      partFile = sampleDir+"/zobov_slice_"+sample.fullName
+      File = file(partFile)
+      chk = np.fromfile(File, dtype=np.int32,count=1)
+      Np = np.fromfile(File, dtype=np.int32,count=1)
+      chk = np.fromfile(File, dtype=np.int32,count=1)
+
+      # x
+      chk = np.fromfile(File, dtype=np.int32,count=1)
+      redshifts = np.fromfile(File, dtype=np.float32,count=Np)
+      chk = np.fromfile(File, dtype=np.int32,count=1)
+
+      # y
+      chk = np.fromfile(File, dtype=np.int32,count=1)
+      redshifts = np.fromfile(File, dtype=np.float32,count=Np)
+      chk = np.fromfile(File, dtype=np.int32,count=1)
+
+      # z
+      chk = np.fromfile(File, dtype=np.int32,count=1)
+      redshifts = np.fromfile(File, dtype=np.float32,count=Np)
+      chk = np.fromfile(File, dtype=np.int32,count=1)
+
+      # RA
+      chk = np.fromfile(File, dtype=np.int32,count=1)
+      redshifts = np.fromfile(File, dtype=np.float32,count=Np)
+      chk = np.fromfile(File, dtype=np.int32,count=1)
+
+      # Dec
+      chk = np.fromfile(File, dtype=np.int32,count=1)
+      redshifts = np.fromfile(File, dtype=np.float32,count=Np)
+      chk = np.fromfile(File, dtype=np.int32,count=1)
+
+      # z
+      chk = np.fromfile(File, dtype=np.int32,count=1)
+      redshifts = np.fromfile(File, dtype=np.float32,count=Np)
+      chk = np.fromfile(File, dtype=np.int32,count=1)
+      File.close()
+      
+      # build selection function interpolation
+      selfuncData = np.genfromtxt(sample.selFunFile)
+      selfunc = interpolate.interp1d(selfuncData[:,0], selfuncData[:,1],
+                                     kind='cubic')
+      # re-weight and write
+      vols *= selfunc(redshifts)
+
+      volFile = zobovDir+"/vol_"+sampleName+".dat"
+      File = file(volFile, 'w')
+      chk.astype('np.int32').tofile(File)
+      vols.astype('np.float32').tofile(File)
+
+      volFileToUse = zobovDir+"/vol_weighted"+sampleName+".dat"
+    else:
+      volFileToUse = zobovDir+"/vol_"+sampleName+".dat"
 
 
     cmd = [binPath+"../c_tools/zobov2/jozov2/jozov2", \
            zobovDir+"/adj_"+sampleName+".dat", \
-           zobovDir+"/vol_weighted_"+sampleName+".dat", \
-           #zobovDir+"/vol_"+sampleName+".dat", \
+           volFileToUse, \
            zobovDir+"/voidPart_"+sampleName+".dat", \
            zobovDir+"/voidZone_"+sampleName+".dat", \
            zobovDir+"/voidDesc_"+sampleName+".out", \

python_tools/void_python_tools/voidUtil/catalogUtil.py

@@ -456,9 +456,13 @@ def getArray(objectList, attr):
   if hasattr(objectList[0], attr):
     ndim = np.shape( np.atleast_1d( getattr(objectList[0], attr) ) )[0]
     attrArr = np.zeros(( len(objectList), ndim ))
+    }
     for idim in xrange(ndim):
       attrArr[:,idim] = np.fromiter((np.atleast_1d(getattr(v, attr))[idim] \
                                     for v in objectList), float )
+  
+    if ndim == 1: attrArr = attArr[:,0]
+
     return attrArr
   else:
     print " Attribute", attr, "not found!"

python_tools/void_python_tools/voidUtil/plotUtil.py

@@ -25,7 +25,7 @@ import numpy as np
 import os
 import pylab as plt
 import void_python_tools.apTools as vp
-from void_python_tools.voidUtil import getArray
+from void_python_tools.voidUtil import getArray, shiftPart, getVoidPart
 
 def fill_between(x, y1, y2=0, ax=None, **kwargs):
     """Plot filled region between `y1` and `y2`.
@@ -183,7 +183,7 @@ def plotEllipDist(catalogList,
 
 
 # -----------------------------------------------------------------------------
-def plotVoidCells(catalogList,
+def plotVoidCells(catalog,
               voidID,
               figDir="./",
               plotName="cells",