getting rid of funky center coordinated for observations

c_tools/stacking/pruneVoids.cpp

@@ -1102,12 +1102,11 @@ void outputVoids(string outputDir, string sampleName, string prefix,
      outCenter[1] = outVoid.barycenter[1];
      outCenter[2] = outVoid.barycenter[2];
 
-     if (isObservation) {
+     //if (isObservation) {
-       outCenter[0] = (outVoid.barycenter[0]-boxLen[0]/2.)*100.;
+     //  outCenter[0] = (outVoid.barycenter[0]-boxLen[0]/2.)*100.;
-       outCenter[1] = (outVoid.barycenter[1]-boxLen[1]/2.)*100.;
+     //  outCenter[1] = (outVoid.barycenter[1]-boxLen[1]/2.)*100.;
-       outCenter[2] = (outVoid.barycenter[2]-boxLen[2]/2.)*100.;
+     //  outCenter[2] = (outVoid.barycenter[2]-boxLen[2]/2.)*100.;
-     }
+     //}
-
 
      fprintf(fpZobov, "%d %d %d %f %f %d %d %f %d %f %f\n", 
              iVoid, 

python_tools/void_python_tools/__init__.py

@@ -21,3 +21,4 @@ from void_python_tools.backend  import *
 from void_python_tools.apTools  import *
 from void_python_tools.plotting import *
 from void_python_tools.xcor     import *
+from void_python_tools.partUtil import *

python_tools/void_python_tools/partUtil/__init__.py

@@ -0,0 +1,20 @@
+#+
+#   VIDE -- Void IDentification and Examination -- ./python_tools/void_python_tools/plotting/__init__.py
+#   Copyright (C) 2010-2013 Guilhem Lavaux
+#   Copyright (C) 2011-2013 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 partUtil import *

python_tools/void_python_tools/partUtil/partUtil.py

@@ -0,0 +1,127 @@
+#+
+#   VIDE -- Void IDentification and Examination -- ./python_tools/void_python_tools/plotting/__init__.py
+#   Copyright (C) 2010-2013 Guilhem Lavaux
+#   Copyright (C) 2011-2013 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.
+#+
+
+# Various utilities for loading and modifying particle datasets
+
+import numpy as np
+from netCDF4 import Dataset
+import sys
+from void_python_tools.backend import *
+import void_python_tools.apTools as vp
+
+NetCDFFile = Dataset
+ncFloat = 'f8'
+
+# -----------------------------------------------------------------------------
+def loadPart(workDir, sampleDir, sample):
+    #print "    Loading particle data..."
+    sys.stdout.flush()
+
+    infoFile = workDir+"/"+sampleDir+"/zobov_slice_"+sample.fullName+".par"
+    File = NetCDFFile(infoFile, 'r')
+    ranges = np.zeros((3,2))
+    ranges[0][0] = getattr(File, 'range_x_min')
+    ranges[0][1] = getattr(File, 'range_x_max')
+    ranges[1][0] = getattr(File, 'range_y_min')
+    ranges[1][1] = getattr(File, 'range_y_max')
+    ranges[2][0] = getattr(File, 'range_z_min')
+    ranges[2][1] = getattr(File, 'range_z_max')
+    isObservation = getattr(File, 'is_observation')
+    maskIndex = getattr(File, 'mask_index')
+    File.close()
+    mul = np.zeros((3))
+    mul[:] = ranges[:,1] - ranges[:,0]
+
+    partFile = workDir+"/"+sampleDir+"/zobov_slice_"+sample.fullName
+    iLine = 0
+    partData = []
+    part = np.zeros((3))
+    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)
+
+    chk = np.fromfile(File, dtype=np.int32,count=1)
+    x = np.fromfile(File, dtype=np.float32,count=Np)
+    x *= mul[0]
+    if isObservation != 1:
+      x += ranges[0][0]
+    chk = np.fromfile(File, dtype=np.int32,count=1)
+
+    chk = np.fromfile(File, dtype=np.int32,count=1)
+    y = np.fromfile(File, dtype=np.float32,count=Np)
+    y *= mul[1] 
+    if isObservation != 1:
+      y += ranges[1][0]
+    chk = np.fromfile(File, dtype=np.int32,count=1)
+
+    chk = np.fromfile(File, dtype=np.int32,count=1)
+    z = np.fromfile(File, dtype=np.float32,count=Np)
+    z *= mul[2] 
+    if isObservation != 1:
+      z += ranges[2][0]
+    chk = np.fromfile(File, dtype=np.int32,count=1)
+    File.close()
+
+    if isObservation == 1:
+      x = x[0:maskIndex]# * 100/300000
+      y = y[0:maskIndex]# * 100/300000
+      z = z[0:maskIndex]# * 100/300000
+
+    partData = np.column_stack((x,y,z))
+
+    boxLen = mul
+
+    if isObservation == 1:
+      props = vp.getSurveyProps(sample.maskFile, sample.zBoundary[0],
+                                sample.zBoundary[1], 
+                                sample.zBoundary[0], 
+                                sample.zBoundary[1], "all",
+                                useLCDM=sample.useLCDM)
+      boxVol = props[0]
+      volNorm = maskIndex/boxVol
+    else:
+      boxVol = np.prod(boxLen) 
+      volNorm = len(x)/boxVol
+
+    isObservationData = isObservation == 1
+
+    return partData, boxLen, volNorm, isObservationData
+
+# -----------------------------------------------------------------------------
+def shiftPart(inPart, newCenter, periodicLine, boxLen):
+
+  part = inPart.copy()
+
+  part[:,0] -= newCenter[0]
+  part[:,1] -= newCenter[1]
+  part[:,2] -= newCenter[2]
+
+  shiftUs = np.abs(part[:,0]) > boxLen[0]/2.
+  if ("x" in periodicLine): part[shiftUs,0] -= \
+                            np.copysign(boxLen[0], part[shiftUs,0])
+  shiftUs = np.abs(part[:,1]) > boxLen[1]/2.
+  if ("y" in periodicLine): part[shiftUs,1] -= \
+                            np.copysign(boxLen[1], part[shiftUs,1])
+  shiftUs = np.abs(part[:,2]) > boxLen[2]/2.
+  if ("z" in periodicLine): part[shiftUs,2] -= \
+                            np.copysign(boxLen[2], part[shiftUs,2])
+
+  return part