updated plotting

README

@@ -16,50 +16,4 @@ Copyright (C) 2010-2014 Guilhem Lavaux, 2011-2014 P.M. Sutter.
 This software is put under the GNU Public License. Please see LICENSE
 for further information.
 
-
-Parts of the pipeline includes ZOBOV. See zobov/zobov_readme.txt for 
-copyright/license information
-
-Building
---------
-
-
-After compiling, go to the pipeline directory.
-
-
-Using the pipeline
-------------------
-
-
-Create a dataset parameter file. Look at datasets/multidark.py for 
-an example. Describe the simulation, where to put outputs, how many 
-redshift slices, subvolumes, etc. etc.
-
-prepareCatalogs will produce a pipeline script for each
-subsampling you choose. If you have multiple redshift particle files,
-and choose multiple slices and/or subdivisions, they will be packaged
-in the same pipeline script.
-
-Run "./generateCatalog.py [name of pipeline script]" for each script
-written by prepareGadgetCatalog. This will run generateMock, zobov,
-and pruneVoids. At the end of it, you should have a void catalog for
-each redshift, slice, and subdivision.
-
-Check the logfiles for any error messages.
-
-See the README of the public void catalog for the format of the
-outputs.
-
-Please do not change the outputs of pruneVoids etc. without
-discussion, since further analysis relies on the current formats.
-
-If you're wondering why these scripts are rather complex, it's because
-it can also support A-P analysis, which is much more complicated :)
-
-Good luck!
-
-Important directories:
-
-pipeline: scripts to set up and generate void catalogs
-crossCompare: analysis and plotting tools designed to work with disparate catalogs
-
+This pipeline includes ZOBOV. See zobov/zobov_readme.txt for copyright/license information.

python_tools/void_python_tools/voidUtil/__init__.py

@@ -17,4 +17,7 @@
 #   with this program; if not, write to the Free Software Foundation, Inc.,
 #   51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
 #+
+
 from catalogUtil import *
+from plotDefs import *
+from plotUtil import *

python_tools/void_python_tools/voidUtil/plotDefs.py

@@ -0,0 +1,33 @@
+#+
+#   VIDE -- Void IDentification and Examination -- ./python_tools/void_python_tools/plotting/plotDefs.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.
+#+
+LIGHT_SPEED = 299792.458 
+
+colorList = ['r', 'b', 'g', 'y', 'c', 'm', 
+             'darkred', 'grey',
+             'orange', 'darkblue',
+             'indigo', 'lightseagreen', 'maroon', 'olive',
+             'royalblue', 'palevioletred', 'seagreen', 'tomato',
+             'aquamarine', 'darkslateblue',
+             'khaki', 'lawngreen', 'mediumorchid',
+             'orangered', 'thistle'
+             'yellowgreen']
+
+linewidth = 4
+fontsize = 12

python_tools/void_python_tools/voidUtil/plotUtil.py

@@ -0,0 +1,121 @@
+#+
+#   VIDE -- Void IDentification and Examination -- ./python_tools/void_python_tools/plotting/plotTools.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.
+#+
+__all__=['plotRedshiftDistribution', 'plotSizeDistribution', 'plot1dProfiles',
+         'plotMarg1d', 'plotNumberDistribution', 'plotVoidDistribution']
+
+from void_python_tools.backend.classes import *
+from plotDefs import *
+import numpy as np
+import os
+import pylab as plt
+import void_python_tools.apTools as vp
+
+def fill_between(x, y1, y2=0, ax=None, **kwargs):
+    """Plot filled region between `y1` and `y2`.
+
+    This function works exactly the same as matplotlib's fill_between, except
+    that it also plots a proxy artist (specifically, a rectangle of 0 size)
+    so that it can be added it appears on a legend.
+    """
+    ax = ax if ax is not None else plt.gca()
+    ax.fill_between(x, y1, y2, interpolate=True, **kwargs)
+    p = plt.Rectangle((0, 0), 0, 0, **kwargs)
+    ax.add_patch(p)
+
+# -----------------------------------------------------------------------------
+def plotNumberFunction(sampleDirList=None, figDir="./", 
+                       plotName="numberfunc", 
+                       dataPortion="central"):
+
+print "Plotting number function"
+
+plt.clf()
+plt.xlabel("$R_{eff}$ [$h^{-1}Mpc$]", fontsize=14)
+plt.ylabel(r"log ($n$ (> R) [$h^3$ Gpc$^{-3}$])", fontsize=14)
+
+for (iSample,sampleDir) in enumerate(sampleDirList):
+  with open(workDir+sampleDir+"/sample_info.dat", 'rb') as input:
+    sample = pickle.load(input)
+  filename = sampleDir+"/centers_"+dataPortion+"_"+sample.fullName+".out"
+  if not os.access(filename, os.F_OK):
+    print "File not found: ", filename
+  else:
+    data = np.loadtxt(filename, comments="#")[:,4]
+
+  if sample.dataType == "observation":
+    # look for the mask file
+    if os.access(sample.maskFile, os.F_OK):
+      maskFile = sample.maskFile
+    else:
+      maskFile = sampleDir+"/"+os.path.basename(sample.maskFile)
+      print "Using maskfile found in:", maskFile
+
+    boxVol = vp.getSurveyProps(maskFile,
+                               sample.zBoundary[0], sample.zBoundary[1],
+                               sample.zRange[0], sample.zRange[1], "all",
+                               selectionFuncFile=None)[0]
+                               #selectionFuncFile=sample.selFunFile)[0]
+    boxVol *= obsFudgeFactor
+  else:
+    boxVol = sample.boxLen*sample.boxLen*(sample.zBoundaryMpc[1] -
+                                          sample.zBoundaryMpc[0])
+
+  boxVol *= 1.e-9 # Mpc->Gpc
+
+  bins = args.xmax/5.
+  hist, binEdges = np.histogram(data, bins=bins, range=(0., 100.))
+  binCenters = 0.5*(binEdges[1:] + binEdges[:-1])
+
+  nvoids = len(data)
+  var = hist * (1. - hist/nvoids)
+  sig = np.sqrt(var)
+
+  lowerbound = hist - sig
+  upperbound = hist + sig
+
+  mean = np.log10(hist/boxVol)
+  lowerbound = np.log10(lowerbound/boxVol)
+  upperbound = np.log10(upperbound/boxVol)
+
+  lineColor = colorList[iSample]
+  lineTitle = sample.fullName
+  
+  trim = (bounds[0] > .01)
+  mean = mean[trim]
+  binCentersToUse = binCenters[trim]
+  lower = lowerbound[trim]
+  upper = upperbound[trim]
+
+  alpha = 0.55
+  fill_between(binCentersToUse, lower, upper,
+             label=lineTitle, color=lineColor,
+             alpha=alpha,
+             )
+
+  lineStyle = '-'
+  plt.plot(binCentersToUse, mean, lineStyle,
+              color=lineColor,
+              linewidth=3)
+
+  plt.legend(loc = "upper right", fancybox=True, prop={'size':14})
+
+  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")