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348 lines
11 KiB
Python
348 lines
11 KiB
Python
#+
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# VIDE -- Void IDentification and Examination -- ./python_tools/void_python_tools/plotting/__init__.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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# Various utilities for loading and modifying particle datasets
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import numpy as np
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from netCDF4 import Dataset
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import sys
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from void_python_tools.backend import *
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import void_python_tools.apTools as vp
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import pickle
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from periodic_kdtree import PeriodicCKDTree
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import os
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NetCDFFile = Dataset
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ncFloat = 'f8'
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# -----------------------------------------------------------------------------
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def loadPart(sampleDir):
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print " Loading particle data..."
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sys.stdout.flush()
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with open(sampleDir+"/sample_info.dat", 'rb') as input:
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sample = pickle.load(input)
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infoFile = 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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isObservation = getattr(File, 'is_observation')
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maskIndex = getattr(File, 'mask_index')
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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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partFile = sampleDir+"/zobov_slice_"+sample.fullName
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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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if isObservation != 1:
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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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if isObservation != 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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if isObservation != 1:
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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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if isObservation == 1:
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x = x[0:maskIndex]# * 100/300000
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y = y[0:maskIndex]# * 100/300000
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z = z[0:maskIndex]# * 100/300000
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partData = np.column_stack((x,y,z))
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boxLen = mul
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if isObservation == 1:
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# look for the mask file
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if os.access(sample.maskFile, os.F_OK):
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maskFile = sample.maskFile
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else:
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maskFile = sampleDir+"/"+os.path.basename(sample.maskFile)
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print "Using maskfile found in:", maskFile
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props = vp.getSurveyProps(maskFile, sample.zBoundary[0],
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sample.zBoundary[1],
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sample.zBoundary[0],
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sample.zBoundary[1], "all",
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useLCDM=sample.useComoving)
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boxVol = props[0]
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volNorm = maskIndex/boxVol
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else:
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boxVol = np.prod(boxLen)
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volNorm = len(x)/boxVol
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isObservationData = isObservation == 1
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return partData, boxLen, volNorm, isObservationData, ranges
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# -----------------------------------------------------------------------------
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def loadPartVel(sampleDir):
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#print " Loading particle velocities..."
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sys.stdout.flush()
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with open(sampleDir+"/sample_info.dat", 'rb') as input:
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sample = pickle.load(input)
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infoFile = sampleDir+"/zobov_slice_"+sample.fullName+".par"
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File = NetCDFFile(infoFile, 'r')
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isObservation = getattr(File, 'is_observation')
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if isObservation:
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print "No velocities for observations!"
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return -1
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vx = File.variables['vel_x'][0:]
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vy = File.variables['vel_y'][0:]
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vz = File.variables['vel_z'][0:]
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File.close()
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partVel = np.column_stack((vx,vy,vz))
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return partVel
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# -----------------------------------------------------------------------------
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def getPartTree(sampleDir, partData, boxLen):
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with open(sampleDir+"/sample_info.dat", 'rb') as input:
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sample = pickle.load(input)
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periodicLine = getPeriodic(sample)
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periodic = 1.*boxLen
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if not "x" in periodicLine: periodic[0] = -1
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if not "y" in periodicLine: periodic[1] = -1
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if not "z" in periodicLine: periodic[2] = -1
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return PeriodicCKDTree(periodic, partData)
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# -----------------------------------------------------------------------------
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def getBall(partTree, center, radius):
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return partTree.query_ball_point(center, r=radius)
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# -----------------------------------------------------------------------------
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def shiftPart(inPart, center, periodicLine, ranges):
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part = inPart.copy()
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newCenter = 1.*center;
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boxLen = np.zeros((3))
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boxLen[0] = ranges[0][1] - ranges[0][0]
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boxLen[1] = ranges[1][1] - ranges[1][0]
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boxLen[2] = ranges[2][1] - ranges[2][0]
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# shift to box coordinates
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part[:,0] -= ranges[0][0]
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part[:,1] -= ranges[1][0]
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part[:,2] -= ranges[2][0]
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newCenter[:] -= ranges[:,0]
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part[:,0] -= newCenter[0]
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part[:,1] -= newCenter[1]
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part[:,2] -= newCenter[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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#part[:,0] += ranges[0][0]
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#part[:,1] += ranges[1][0]
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#part[:,2] += ranges[2][0]
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return part
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# -----------------------------------------------------------------------------
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class Bunch:
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def __init__(self, **kwds):
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self.__dict__.update(kwds)
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class Catalog:
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numVoids = 0
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numPartTot = 0
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numZonesTot = 0
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boxLen = np.zeros((3))
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part = None
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zones2Parts = None
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void2Zones = None
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voids = None
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# -----------------------------------------------------------------------------
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def loadVoidCatalog(sampleDir):
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#print " Loading particle data..."
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sys.stdout.flush()
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catalog = Catalog()
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with open(sampleDir+"/sample_info.dat", 'rb') as input:
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sample = pickle.load(input)
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print "Loading info..."
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infoFile = 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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catalog.boxLen[0] = ranges[0][1] - ranges[0][0]
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catalog.boxLen[1] = ranges[1][1] - ranges[1][0]
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catalog.boxLen[2] = ranges[2][1] - ranges[2][0]
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File.close()
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print "Loading all particles..."
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partData, boxLen, volNorm, isObservationData, ranges = loadPart(sampleDir)
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numPartTot = len(partData)
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catalog.numPartTot = numPartTot
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catalog.part = []
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for i in xrange(len(partData)):
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catalog.part.append(Bunch(x = partData[i][0],
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y = partData[i][1],
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z = partData[i][2],
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volume = 0,
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ra = 0,
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dec = 0,
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redshift = 0,
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uniqueID = 0))
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print "Loading volumes..."
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volFile = sampleDir+"/vol_"+sample.fullName+".dat"
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File = file(volFile)
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chk = np.fromfile(File, dtype=np.int32,count=1)
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vols = np.fromfile(File, dtype=np.float32,count=numPartTot)
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for ivol in xrange(len(vols)):
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catalog.part[ivol].volume = vols[ivol] / volNorm
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print "Loading voids..."
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fileName = sampleDir+"/voidDesc_central_"+sample.fullName+".out"
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catData = np.loadtxt(fileName, comments="#", skiprows=2)
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catalog.voids = []
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for line in catData:
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catalog.voids.append(Bunch(iVoid = int(line[0]),
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voidID = int(line[1]),
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coreParticle = line[2],
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coreDens = line[3],
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zoneVol = line[4],
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zoneNumPart = line[5],
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numZones = int(line[6]),
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voidVol = line[7],
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numPart = int(line[8]),
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densCon = line[9],
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voidProp = line[10],
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radius = pow(line[7]/volNorm*3./4./np.pi, 1./3.),
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barycenter = np.zeros((3))))
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print "Read %d voids" % len(catalog.voids)
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print "Loading barycenters..."
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iLine = 0
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for line in open(sampleDir+"/barycenters_central_"+sample.fullName+".out"):
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line = line.split()
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catalog.voids[iLine].barycenter[0] = float(line[1])
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catalog.voids[iLine].barycenter[1] = float(line[2])
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catalog.voids[iLine].barycenter[2] = float(line[3])
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iLine += 1
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print "Loading zone-void membership info..."
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zoneFile = sampleDir+"/voidZone_"+sample.fullName+".dat"
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catalog.void2Zones = []
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File = file(zoneFile)
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numZonesTot = np.fromfile(File, dtype=np.int32,count=1)
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catalog.numZonesTot = numZonesTot
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for iZ in xrange(numZonesTot):
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numZones = np.fromfile(File, dtype=np.int32,count=1)
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catalog.void2Zones.append(Bunch(numZones = numZones,
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zoneIDs = []))
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for p in xrange(numZones):
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zoneID = np.fromfile(File, dtype=np.int32,count=1)
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catalog.void2Zones[iZ].zoneIDs.append(zoneID)
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print "Loading particle-zone membership info..."
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zonePartFile = sampleDir+"/voidPart_"+sample.fullName+".dat"
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catalog.zones2Parts = []
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File = file(zonePartFile)
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chk = np.fromfile(File, dtype=np.int32,count=1)
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numZonesTot = np.fromfile(File, dtype=np.int32,count=1)
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for iZ in xrange(numZonesTot):
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numPart = np.fromfile(File, dtype=np.int32,count=1)
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catalog.zones2Parts.append(Bunch(numPart = numPart,
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partIDs = []))
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for p in xrange(numPart):
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partID = np.fromfile(File, dtype=np.int32,count=1)
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catalog.zones2Parts[iZ].partIDs.append(partID)
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return catalog
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# -----------------------------------------------------------------------------
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def getVoidPart(catalog, voidID):
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partOut = []
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for iZ in xrange(catalog.void2Zones[voidID].numZones):
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zoneID = catalog.void2Zones[voidID].zoneIDs[iZ]
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for p in xrange(catalog.zones2Parts[zoneID].numPart):
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partID = catalog.zones2Parts[zoneID].partIDs[p]
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partOut.append(catalog.part[partID])
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return partOut
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