added more tools and plotting for cross-comparison catalog analysis

crossCompare/plotting/plotCocenterProfiles.py

@@ -0,0 +1,174 @@
+#!/usr/bin/env python
+#+
+#   VIDE -- Void IDEntification pipeline -- ./pipeline/apAnalysis.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.
+#+
+
+# plots radial density profiles centered on baseVoid.
+#   requires makeCocenteredProfiles to be run first!
+
+import imp
+import pickle
+import os
+import numpy as np
+import argparse
+import matplotlib
+matplotlib.use('Agg')
+import matplotlib.pyplot as plt
+from void_python_tools.backend import *
+from util import *
+from globalOptions import *
+from scipy.optimize import curve_fit
+
+matplotlib.rcParams.update({'font.size': 20})
+
+# ------------------------------------------------------------------------------
+
+parser = argparse.ArgumentParser(description='Analyze.')
+parser.add_argument('--parm', dest='parm', default='datasetsToAnalyze.py', help='path to parameter file')
+parser.add_argument('--show', dest='showPlot', action='store_const',
+                   const=True, default=False,
+                   help='display the plot (default: just write eps)')
+args = parser.parse_args()
+
+# -----------------------------------------------------------------------------
+# Lavaux & Wandelt (2012) profile
+def LWProfile(r, A0, A3, alpha):
+  return A0 + A3*r**3.
+  #return A0 + A3*r**alpha
+
+# -----------------------------------------------------------------------------
+# http://arxiv.org/pdf/astro-ph/0508297v1.pdf eq. 5
+def PadillaProfile(r, A1, A2, alpha):
+  return 1.5-A1*np.exp(-(A2*r)**alpha)
+
+
+# -----------------------------------------------------------------------------
+# plot a slice of the density around the void in baseIDList, 
+#   with any voids in the slice shown and any voids in baseIDList flagged
+def plotProfiles(baseSample, stack, sampleList,
+                 figDir, showPlot, outputDir, doTheory):
+
+  thisRadius = str(stack.rMin) + "-" + str(stack.rMax)
+  plotName = "1dprofile_cocenter_" + baseSample.fullName+"_"+thisRadius
+
+  filename = "1dprofile_cocenter_" + baseSample.fullName+"_"+thisRadius
+  npzfile = np.load(outputDir+"/1dprofile_cocentered_"+plotName+".dat.npz")
+  profileList = npzfile['arr_0']
+  radii = npzfile['arr_1']
+
+  plt.clf()
+
+  plt.xlabel(r"$R/R_{eff}$")
+  #plt.xlabel(r"$R/R_{v,\mathrm{max}}$")
+  plt.ylabel(r"$n / \bar n$")
+  plt.xlim(xmin=0.0, xmax=2.5)
+  plt.ylim(ymin=0.0, ymax=1.7)
+  #plt.xscale('log')
+
+  for (iSample, sample) in enumerate(sampleList):
+    lineTitle = sample.nickName[:-10]
+    if "DM LowDen" in lineTitle or "DM HighDen" in lineTitle: continue
+
+    thisPlotTitle = r"$R_{eff}$ = "+thisRadius+ r" $h^{-1}$Mpc"
+    legendTitle = "Fixed Center Samples"
+
+    thisProfile = profileList[iSample]
+    if np.all(thisProfile == 0.): continue
+
+    rV = (stack.rMin + stack.rMax)/2.
+
+    if len(radii) > 0:
+      scaledRadii = radii/rV
+      plt.plot(scaledRadii, thisProfile, label=lineTitle, 
+               color=colorList[iSample],
+               linewidth=linewidth)
+
+      if doTheory:
+        nBins = len(scaledRadii)/2
+        try:
+          popt, pcov = curve_fit(PadillaProfile, scaledRadii[0:nBins],
+                             thisProfile[0:nBins], maxfev=10000, xtol=5.e-3)
+        except RuntimeError:
+          print "Warning: no convergence reached"
+
+        label = r"A1=%.2f, A2=%.2f, $\alpha$=%.2f" % (popt[0], popt[1], popt[2])
+        rho = PadillaProfile(scaledRadii, popt[0], popt[1], popt[2])
+        plt.plot(scaledRadii, rho, '--', label=label,
+                 color=colorList[iSample], linewidth=2)
+
+
+  plt.title(thisPlotTitle + " (center from " + plotTitle + ")", fontsize=18)
+  plt.legend(title = legendTitle, loc = "lower right", prop={'size':16})
+
+  plt.savefig(figDir+"/fig_"+plotName+".pdf", bbox_inches="tight")
+  plt.savefig(figDir+"/fig_"+plotName+".eps", bbox_inches="tight")
+  plt.savefig(figDir+"/fig_"+plotName+".png", bbox_inches="tight")
+
+  if (showPlot):
+    os.system("display %s" % figDir+"/fig_"+plotName+".png")
+
+  return
+
+# -----------------------------------------------------------------------------
+
+filename = args.parm
+print " Loading parameters from", filename
+if not os.access(filename, os.F_OK):
+  print "  Cannot find parameter file %s!" % filename
+  exit(-1)
+parms = imp.load_source("name", filename)
+globals().update(vars(parms))
+
+if not os.access(outputDir, os.F_OK):
+  os.makedirs(outputDir)
+
+if not os.access(logDir, os.F_OK):
+  os.makedirs(logDir)
+
+if not os.access(figDir, os.F_OK):
+  os.makedirs(figDir)
+
+# get list of base voids
+with open(workDir+baseSampleDir+"/sample_info.dat", 'rb') as input:
+  baseSample = pickle.load(input)
+  baseSampleName = baseSample.fullName
+  baseVoidList = np.loadtxt(workDir+baseSampleDir+"/centers_central_"+\
+                    baseSampleName+".out")
+
+sampleList = []
+for sampleDir in sampleDirList:
+  if compareSampleTag in sampleDir: continue
+  with open(workDir+sampleDir+"/sample_info.dat", 'rb') as input:
+    sampleList.append(pickle.load(input))
+
+sampleDirList.insert(0,baseSampleDir)
+sampleList.insert(0,baseSample)
+
+# pick our void sample
+for stack in baseSample.stacks:
+  print " Stack:", stack.rMin, "-", stack.rMax
+
+  # plot these profiles
+  print "  Plotting..."
+  sys.stdout.flush()
+  plotProfiles(baseSample, stack, sampleList,
+               figDir, args.showPlot, outputDir, doTheory)
+    
+print " Done!"
+