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https://bitbucket.org/cosmicvoids/vide_public.git
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added more tools and plotting for cross-comparison catalog analysis
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parent
4ac04bbde5
commit
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10 changed files with 1224 additions and 267 deletions
385
crossCompare/plotting/plotDenMaps.py
Executable file
385
crossCompare/plotting/plotDenMaps.py
Executable file
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#!/usr/bin/env python
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#+
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# VIDE -- Void IDEntification pipeline -- ./pipeline/apAnalysis.py
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# Copyright (C) 2010-2013 Guilhem Lavaux
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# Copyright (C) 2011-2013 P. M. Sutter
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#
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# This program is free software; you can redistribute it and/or modify
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# it under the terms of the GNU General Public License as published by
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# the Free Software Foundation; version 2 of the License.
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#
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#
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# This program is distributed in the hope that it will be useful,
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# but WITHOUT ANY WARRANTY; without even the implied warranty of
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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# GNU General Public License for more details.
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#
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# You should have received a copy of the GNU General Public License along
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# with this program; if not, write to the Free Software Foundation, Inc.,
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# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
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#+
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# takes nVoids evenly distributed, plots a slice of the local density and
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# overlays the voids
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import imp
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import pickle
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import os
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import numpy as np
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import argparse
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import matplotlib
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matplotlib.use('Agg')
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import matplotlib.pyplot as plt
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from void_python_tools.backend import *
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import void_python_tools.xcor as xcor
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from netCDF4 import Dataset
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#import pylab as plt
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NetCDFFile = Dataset
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ncFloat = 'f8'
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matplotlib.rcParams.update({'font.size': 16})
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# ------------------------------------------------------------------------------
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mergerNameBase = "voidOverlap"
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parser = argparse.ArgumentParser(description='Analyze.')
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parser.add_argument('--parm', dest='parm', default='datasetsToAnalyze.py', help='path to parameter file')
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parser.add_argument('--show', dest='showPlot', action='store_const',
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const=True, default=False,
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help='display the plot (default: just write eps)')
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args = parser.parse_args()
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nVoids = 10
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# ------------------------------------------------------------------------------
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# -----------------------------------------------------------------------------
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# plot a slice of the density around the void in baseIDList,
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# with any voids in the slice shown and any voids in baseIDList flagged
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def plotVoidAndDen(idList, voidList, partData, boxLen, figDir,
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sliceCenter=None, sliceWidth=200,
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baseIDList=None, baseRadius=0, nickName=None,
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baseNickName=None,
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baseIndex=0,
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periodic=None, showPlot=False, plotName=None):
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if len(voidList) <= 1: return
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plt.clf()
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#sliceWidth = 220
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sliceWidth = max(220, sliceWidth)
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# make an appropriate box
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xwidth = sliceWidth
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ywidth = sliceWidth
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zwidth = sliceWidth/4.
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#zwidth = max(sliceWidth/4., 50)
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# get mean density
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part = 1.*partData
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totalNumPart = len(part)
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totalVol = (part[:,0].max() - part[:,0].min()) * \
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(part[:,1].max() - part[:,1].min()) * \
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(part[:,2].max() - part[:,2].min())
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meanDen = totalNumPart/totalVol
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# single out the matched void
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keepVoid = []
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if len(np.atleast_1d(idList)) > 0:
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keepVoid = voidList[voidList[:,7] == idList]
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if len(np.shape(keepVoid)) > 1: keepVoid = keepVoid[0,:]
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filter = voidList[:,7] != idList
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voidList = voidList[filter,:]
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# convert everything to relative coordinates
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part[:,0] -= sliceCenter[0]
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part[:,1] -= sliceCenter[1]
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part[:,2] -= sliceCenter[2]
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shiftUs = np.abs(part[:,0]) > boxLen[0]/2.
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if ("x" in periodicLine): part[shiftUs,0] -= \
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np.copysign(boxLen[0],part[shiftUs,0])
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shiftUs = np.abs(part[:,1]) > boxLen[1]/2.
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if ("y" in periodicLine): part[shiftUs,1] -= \
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np.copysign(boxLen[1],part[shiftUs,1])
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shiftUs = np.abs(part[:,2]) > boxLen[2]/2.
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if ("z" in periodicLine): part[shiftUs,2] -= \
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np.copysign(boxLen[2],part[shiftUs,2])
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voidList = np.atleast_2d(voidList)
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np.atleast_2d(voidList)[:,0] -= sliceCenter[0]
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np.atleast_2d(voidList)[:,1] -= sliceCenter[1]
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np.atleast_2d(voidList)[:,2] -= sliceCenter[2]
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shiftUs = np.abs(voidList[:,0]) > boxLen[0]/2.
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if ("x" in periodicLine):
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voidList[shiftUs,0] -= \
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np.copysign(boxLen[0],voidList[shiftUs,0])
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shiftUs = np.abs(voidList[:,1]) > boxLen[1]/2.
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if ("y" in periodicLine): voidList[shiftUs,1] -= \
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np.copysign(boxLen[1],voidList[shiftUs,1])
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shiftUs = np.abs(voidList[:,2]) > boxLen[2]/2.
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if ("z" in periodicLine): voidList[shiftUs,2] -= \
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np.copysign(boxLen[2],voidList[shiftUs,2])
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if len(np.atleast_1d(keepVoid)) >= 1:
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keepVoid[0] -= sliceCenter[0]
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keepVoid[1] -= sliceCenter[1]
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keepVoid[2] -= sliceCenter[2]
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shiftUs = np.abs(keepVoid[0]) > boxLen[0]/2.
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if ("x" in periodicLine) and shiftUs: keepVoid[0] -= \
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np.copysign(boxLen[0],keepVoid[0])
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shiftUs = np.abs(keepVoid[1]) > boxLen[1]/2.
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if ("y" in periodicLine) and shiftUs: keepVoid[1] -= \
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np.copysign(boxLen[1],keepVoid[1])
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shiftUs = np.abs(keepVoid[2]) > boxLen[2]/2.
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if ("z" in periodicLine) and shiftUs: keepVoid[2] -= \
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np.copysign(boxLen[2],keepVoid[2])
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xmin = -xwidth/2.
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xmax = xwidth/2.
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ymin = -ywidth/2.
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ymax = ywidth/2.
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zmin = -zwidth/2.
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zmax = zwidth/2.
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# pull out voids that were potential matches
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filter = np.sqrt(voidList[:,0]**2 + voidList[:,1]**2 + voidList[:,2]**2) <=\
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baseRadius*1.5
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potentialMatches = voidList[filter]
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# get centers and radii of any other voids in slice
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zminVoid = -zwidth/16.
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zmaxVoid = zwidth/16.
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filter = (voidList[:,0] > xmin) & (voidList[:,0] < xmax) & \
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(voidList[:,1] > ymin) & (voidList[:,1] < ymax) & \
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(voidList[:,2] > zminVoid) & (voidList[:,2] < zmaxVoid)
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voidList = voidList[filter,:]
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# slice particles
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filter = (part[:,0] > xmin) & (part[:,0] < xmax) & \
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(part[:,1] > ymin) & (part[:,1] < ymax) & \
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(part[:,2] > zmin) & (part[:,2] < zmax)
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part = part[filter]
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# plot density
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extent = [xmin, xmax, ymin, ymax]
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hist, xedges, yedges = np.histogram2d(part[:,0], part[:,1], normed=False,
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bins=64)
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#hist /= meanDen
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hist = np.log10(hist+1)
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plt.imshow(hist,
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aspect='equal',
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extent=extent,
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interpolation='gaussian',
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cmap='YlGnBu_r')
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#plt.colorbar()
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# overlay voids as circles
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fig = plt.gcf()
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ax = fig.add_subplot(1,1,1)
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# the original void
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circle = plt.Circle((0,0), baseRadius,
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edgecolor='orange', facecolor=None, fill=False,
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linewidth=5)
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fig.gca().add_artist(circle)
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# our matched void
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if len(np.atleast_1d(keepVoid)) > 0:
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if idList == baseIDList:
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edgecolor = 'orange'
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else:
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edgecolor = 'red'
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circle = plt.Circle((keepVoid[0], keepVoid[1]), keepVoid[4],
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edgecolor=edgecolor, facecolor=None, fill=False,
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linewidth=5)
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fig.gca().add_artist(circle)
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# other voids in the slice
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for void in voidList:
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if np.any(void[7] == idList):
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continue
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else:
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color = 'white'
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circle = plt.Circle((void[0], void[1]), void[4],
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edgecolor=color, facecolor=None, fill=False,
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linewidth=5)
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fig.gca().add_artist(circle)
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# potential match voids
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#for void in potentialMatches:
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# if np.any(void[7] == idList):
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# continue
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# else:
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# color = 'green'
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# circle = plt.Circle((void[0], void[1]), void[4],
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# edgecolor=color, facecolor=None, fill=False,
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# linewidth=5)
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# fig.gca().add_artist(circle)
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baseNickName = baseNickName[:-10].lstrip()
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nickName = nickName[:-10].lstrip()
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if idList == baseIDList:
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title = "%d $h^{-1}$Mpc" % int(baseRadius)
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title += " (" + baseNickName + ")"
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else:
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title = r"$\rightarrow$ "
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if len(np.atleast_1d(keepVoid)) > 0:
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title += "%d $h^{-1}$Mpc" % int(keepVoid[4]) + " (" + nickName + ")"
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else:
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title += "No match"
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#title += "(" + str(int(baseIDList)) + ")"
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plt.title(title, fontsize=20)
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#plt.xlabel("x [$h^{-1}$Mpc]", fontsize=14)
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#plt.ylabel("y [$h^{-1}$Mpc]", fontsize=14)
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plotName += "_" + str(int(baseIndex))
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#plotName += "_" + str(int(baseRadius))
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plt.savefig(figDir+"/fig_"+plotName+".pdf", bbox_inches="tight")
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plt.savefig(figDir+"/fig_"+plotName+".eps", bbox_inches="tight")
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plt.savefig(figDir+"/fig_"+plotName+".png", bbox_inches="tight")
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if showPlot: os.system("display %s" % figDir+"/fig_"+plotName+".png")
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return
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# -----------------------------------------------------------------------------
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filename = args.parm
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print " Loading parameters from", filename
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if not os.access(filename, os.F_OK):
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print " Cannot find parameter file %s!" % filename
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exit(-1)
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parms = imp.load_source("name", filename)
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globals().update(vars(parms))
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if not os.access(outputDir, os.F_OK):
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os.makedirs(outputDir)
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if not os.access(logDir, os.F_OK):
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os.makedirs(logDir)
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if not os.access(figDir, os.F_OK):
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os.makedirs(figDir)
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mergerFileBase = outputDir + "/" + mergerNameBase
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# get list of base voids
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with open(workDir+baseSampleDir+"/sample_info.dat", 'rb') as input:
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baseSample = pickle.load(input)
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baseSampleName = baseSample.fullName
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baseVoidList = np.loadtxt(workDir+baseSampleDir+"/centers_central_"+\
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baseSampleName+".out")
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# sort by size
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radii = baseVoidList[:,4]
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indices = np.argsort(radii)[::-1]
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baseVoidList = baseVoidList[indices,:]
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setName = baseSampleDir.split('/')[0]
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# pick our void sample
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bigVoidList = baseVoidList[0:10,:]
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stride = len(baseVoidList)/nVoids
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baseVoidList = baseVoidList[::stride]
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baseVoidList = np.vstack((bigVoidList,baseVoidList))
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sampleDirList.insert(0,baseSampleDir)
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for (iSample, sampleDir) in enumerate(sampleDirList):
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if compareSampleTag in sampleDir: continue
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with open(workDir+sampleDir+"/sample_info.dat", 'rb') as input:
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sample = pickle.load(input)
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print " Working with", sample.fullName, "..."
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sys.stdout.flush()
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sampleName = sample.fullName
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print " Loading particle data..."
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sys.stdout.flush()
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infoFile = workDir+"/"+sampleDir+"/zobov_slice_"+sample.fullName+".par"
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File = NetCDFFile(infoFile, 'r')
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ranges = np.zeros((3,2))
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ranges[0][0] = getattr(File, 'range_x_min')
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ranges[0][1] = getattr(File, 'range_x_max')
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ranges[1][0] = getattr(File, 'range_y_min')
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ranges[1][1] = getattr(File, 'range_y_max')
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ranges[2][0] = getattr(File, 'range_z_min')
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ranges[2][1] = getattr(File, 'range_z_max')
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File.close()
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mul = np.zeros((3))
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mul[:] = ranges[:,1] - ranges[:,0]
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boxLen = mul
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partFile = workDir+"/"+sampleDir+"/zobov_slice_"+sample.fullName
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#partFile = catalogDir+"/"+sample.dataFile
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iLine = 0
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partData = []
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part = np.zeros((3))
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File = file(partFile)
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chk = np.fromfile(File, dtype=np.int32,count=1)
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Np = np.fromfile(File, dtype=np.int32,count=1)
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chk = np.fromfile(File, dtype=np.int32,count=1)
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chk = np.fromfile(File, dtype=np.int32,count=1)
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x = np.fromfile(File, dtype=np.float32,count=Np)
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x *= mul[0]
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x += ranges[0][0]
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chk = np.fromfile(File, dtype=np.int32,count=1)
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chk = np.fromfile(File, dtype=np.int32,count=1)
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y = np.fromfile(File, dtype=np.float32,count=Np)
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y *= mul[1]
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y += ranges[1][0]
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chk = np.fromfile(File, dtype=np.int32,count=1)
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chk = np.fromfile(File, dtype=np.int32,count=1)
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z = np.fromfile(File, dtype=np.float32,count=Np)
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z *= mul[2]
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z += ranges[2][0]
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chk = np.fromfile(File, dtype=np.int32,count=1)
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File.close()
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partData = np.column_stack((x,y,z))#.transpose()
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for (iBaseVoid,baseVoid) in enumerate(baseVoidList):
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print " Void:", int(baseVoid[7]), "(", int(baseVoid[4]), ")"
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baseIDList = baseVoid[7]
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sliceCenter = baseVoid[0:3]
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sliceWidth = baseVoid[4]*4
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# get matched void
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idList = []
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if sample.fullName == baseSample.fullName:
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idList = baseIDList
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else:
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matchFile=mergerFileBase+"_"+baseSampleName+"_"+sampleName+"_summary.out"
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if os.access(matchFile, os.F_OK):
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matchList = np.loadtxt(matchFile)
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for i,testID in enumerate(matchList[:,0]):
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if testID == baseIDList:
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if (matchList[i,8] > 0): idList.append(matchList[i,8])
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idList = np.array(idList)
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idList = idList.astype(int)
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voidList = np.loadtxt(workDir+sampleDir+"/trimmed_nodencut_centers_central_"+\
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sampleName+".out")
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periodicLine = getPeriodic(sample)
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plotVoidAndDen(idList, voidList, partData, boxLen, figDir,
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sliceCenter=sliceCenter, sliceWidth=sliceWidth,
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baseIDList=baseIDList, baseRadius=baseVoid[4],
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baseIndex=iBaseVoid,
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nickName=sample.nickName, periodic=periodicLine,
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baseNickName=baseSample.nickName,
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showPlot=args.showPlot,
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plotName="denmap_"+setName+"_"+baseSampleName+"_"+sampleName)
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print " Done!"
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