produce VTK visualizations from postResults files
This commit is contained in:
Philip Eisenlohr
parent
fec2c14a4e
commit
d6edb64929
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@ -20,6 +20,7 @@ bin_link = { \
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],
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],
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'post' : [
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'post' : [
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'postResults',
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'postResults',
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'3Dvisualize',
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'mentat_colorMap',
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'mentat_colorMap',
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],
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],
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}
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}
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@ -0,0 +1,469 @@
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#!/usr/bin/env python
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# -*- coding: UTF-8 no BOM -*-
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# This script is used for the post processing of the results achieved by the spectral method.
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# As it reads in the data coming from "materialpoint_results", it can be adopted to the data
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# computed using the FEM solvers. Until now, its capable to handle elements with one IP in a regular order
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# written by M. Diehl, m.diehl@mpie.de
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import os,sys,threading,re,numpy,time
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from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
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# -----------------------------
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class extendedOption(Option):
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# -----------------------------
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# used for definition of new option parser action 'extend', which enables to take multiple option arguments
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# taken from online tutorial http://docs.python.org/library/optparse.html
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ACTIONS = Option.ACTIONS + ("extend",)
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STORE_ACTIONS = Option.STORE_ACTIONS + ("extend",)
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TYPED_ACTIONS = Option.TYPED_ACTIONS + ("extend",)
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ALWAYS_TYPED_ACTIONS = Option.ALWAYS_TYPED_ACTIONS + ("extend",)
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def take_action(self, action, dest, opt, value, values, parser):
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if action == "extend":
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lvalue = value.split(",")
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values.ensure_value(dest, []).extend(lvalue)
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else:
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Option.take_action(self, action, dest, opt, value, values, parser)
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# -----------------------------
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class backgroundMessage(threading.Thread):
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# -----------------------------
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def __init__(self):
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threading.Thread.__init__(self)
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self.message = ''
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self.new_message = ''
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self.counter = 0
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self.symbols = ['- ', '\ ', '| ', '/ ']
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self.waittime = 0.5
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def __quit__(self):
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length = len(self.message) + len(self.symbols[self.counter])
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sys.stderr.write(chr(8)*length + ' '*length + chr(8)*length)
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sys.stderr.write('')
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def run(self):
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while not threading.enumerate()[0]._Thread__stopped:
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time.sleep(self.waittime)
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self.update_message()
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self.__quit__()
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def set_message(self, new_message):
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self.new_message = new_message
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self.print_message()
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def print_message(self):
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length = len(self.message) + len(self.symbols[self.counter])
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sys.stderr.write(chr(8)*length + ' '*length + chr(8)*length) # delete former message
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sys.stderr.write(self.symbols[self.counter] + self.new_message) # print new message
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self.message = self.new_message
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def update_message(self):
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self.counter = (self.counter + 1)%len(self.symbols)
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self.print_message()
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def outStdout(cmd,locals):
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if cmd[0:3] == '(!)':
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exec(cmd[3:])
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elif cmd[0:3] == '(?)':
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cmd = eval(cmd[3:])
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print cmd
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else:
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print cmd
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return
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def outFile(cmd,locals):
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if cmd[0:3] == '(!)':
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exec(cmd[3:])
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elif cmd[0:3] == '(?)':
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cmd = eval(cmd[3:])
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locals['filepointer'].write(cmd+'\n')
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else:
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locals['filepointer'].write(cmd+'\n')
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return
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def output(cmds,locals,dest):
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for cmd in cmds:
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if isinstance(cmd,list):
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output(cmd,locals,dest)
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else:
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{\
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'File': outFile,\
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'Stdout': outStdout,\
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}[dest](str(cmd),locals)
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return
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#+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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def mesh(res,geomdim,defgrad_av,centroids):
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#+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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neighbor = numpy.array([[0, 0, 0],
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[1, 0, 0],
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[1, 1, 0],
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[0, 1, 0],
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[0, 0, 1],
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[1, 0, 1],
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[1, 1, 1],
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[0, 1, 1]])
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wrappedCentroids = numpy.zeros([res[0]+2,res[1]+2,res[2]+2,3],'d')
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nodes = numpy.zeros([res[0]+1,res[1]+1,res[2]+1,3],'d')
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wrappedCentroids[1:-1,1:-1,1:-1] = centroids
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diag = numpy.ones(3,'i')
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shift = numpy.zeros(3,'i')
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lookup = numpy.zeros(3,'i')
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for k in range(res[2]+2):
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for j in range(res[1]+2):
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for i in range(res[0]+2):
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if (k==0 or k==res[2]+1 or \
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j==0 or j==res[1]+1 or \
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i==0 or i==res[0]+1 ):
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me = numpy.array([i,j,k],'i')
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shift = numpy.sign(res+diag-2*me)*(numpy.abs(res+diag-2*me)/(res+diag))
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lookup = me-diag+shift*res
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wrappedCentroids[i,j,k] = centroids[lookup[0],lookup[1],lookup[2]]- \
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numpy.dot(defgrad_av, shift*geomdim)
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for k in range(res[2]+1):
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for j in range(res[1]+1):
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for i in range(res[0]+1):
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for n in range(8):
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nodes[i,j,k] += wrappedCentroids[i+neighbor[n,0],j+neighbor[n,1],k+neighbor[n,2]]
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nodes[:,:,:] /= 8.0
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return nodes
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# +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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def deformed(res,geomdimension,defgrad):
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# +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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corner = numpy.array([[0, 0, 0],
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[1, 0, 0],
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[1, 1, 0],
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[0, 1, 0],
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[1, 1, 1],
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[0, 1, 1],
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[0, 0, 1],
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[1, 0, 1]])
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step = numpy.array([[ 1, 1, 1],
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[-1, 1, 1],
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[-1,-1, 1],
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[ 1,-1, 1],
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[-1,-1,-1],
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[ 1,-1,-1],
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[ 1, 1,-1],
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[-1, 1,-1]])
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order = numpy.array([[0, 1, 2],
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[0, 2, 1],
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[1, 0, 2],
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[1, 2, 0],
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[2, 0, 1],
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[2, 1, 0]])
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coord = numpy.zeros([8,6,res[0],res[1],res[2],3], 'd')
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coord_avgOrder = numpy.zeros([8,res[0],res[1],res[2],3], 'd')
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coord_avgCorner = numpy.zeros([res[0],res[1],res[2],3], 'd')
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myStep = numpy.zeros(3,'d')
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rear = numpy.zeros(3,'i')
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init = numpy.zeros(3,'i')
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oppo = numpy.zeros(3,'i')
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me = numpy.zeros(3,'i')
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ones = numpy.ones( 3,'i')
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fones = numpy.ones( 3,'d')
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defgrad_av=numpy.average(numpy.average(numpy.average(defgrad,0),0),0)
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for s in range(8): # corners
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init = corner[s]*(res-ones)
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oppo = corner[(s+4)%8]*(res-ones)
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sys.stdout.write('.'*(8-s)+' '*s+'\r')
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sys.stdout.flush()
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for o in range(6): # orders
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for k in range(init[order[o,2]],oppo[order[o,2]]+step[s,order[o,2]],step[s,order[o,2]]):
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rear[order[o,1]] = init[order[o,1]]
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for j in range(init[order[o,1]],oppo[order[o,1]]+step[s,order[o,1]],step[s,order[o,1]]):
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rear[order[o,0]] = init[order[o,0]]
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for i in range(init[order[o,0]],oppo[order[o,0]]+step[s,order[o,0]],step[s,order[o,0]]):
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me[order[o,0]] = i
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me[order[o,1]] = j
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me[order[o,2]] = k
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if (numpy.all(me == init)):
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coord[s,o,me[0],me[1],me[2]] = geomdimension * (numpy.dot(defgrad_av,corner[s]) + \
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numpy.dot(defgrad[me[0],me[1],me[2]],0.5*step[s]/res))
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else:
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myStep = (me-rear)*geomdimension/res
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coord[s,o,me[0],me[1],me[2]] = coord[s,o,rear[0],rear[1],rear[2]] + \
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0.5*numpy.dot(defgrad[me[0],me[1],me[2]] + \
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defgrad[rear[0],rear[1],rear[2]],myStep)
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rear[:] = me[:]
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coord_avgOrder[s] = numpy.average(coord[s],0)
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for k in range(res[2]):
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for j in range(res[1]):
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for i in range(res[0]):
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parameter_coords = (2.0*numpy.array([i,j,k])-res+fones)/(res-fones)
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pos = fones + parameter_coords
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neg = fones - parameter_coords
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coord_avgCorner[i,j,k] = ( coord_avgOrder[0,i,j,k] *neg[0]*neg[1]*neg[2]\
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+ coord_avgOrder[1,i,j,k] *pos[0]*neg[1]*neg[2]\
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+ coord_avgOrder[2,i,j,k] *pos[0]*pos[1]*neg[2]\
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+ coord_avgOrder[3,i,j,k] *neg[0]*pos[1]*neg[2]\
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+ coord_avgOrder[4,i,j,k] *pos[0]*pos[1]*pos[2]\
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+ coord_avgOrder[5,i,j,k] *neg[0]*pos[1]*pos[2]\
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+ coord_avgOrder[6,i,j,k] *neg[0]*neg[1]*pos[2]\
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+ coord_avgOrder[7,i,j,k] *pos[0]*neg[1]*pos[2])*0.125
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print ' '
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return coord_avgCorner, defgrad_av
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# ++++++++++++++++++++++++++++++++++++++++++++++++++++
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def vtk_writeASCII_mesh(mesh,data,res):
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# ++++++++++++++++++++++++++++++++++++++++++++++++++++
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""" function writes data array defined on a hexahedral mesh (geometry) """
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N1 = (res[0]+1)*(res[1]+1)*(res[2]+1)
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N = res[0]*res[1]*res[2]
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cmds = [\
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'# vtk DataFile Version 3.1',
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'powered by 3Dvisualize',
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'ASCII',
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'DATASET UNSTRUCTURED_GRID',
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'POINTS %i float'%N1,
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[[['\t'.join(map(str,mesh[i,j,k])) for i in range(res[0]+1)] for j in range(res[1]+1)] for k in range(res[2]+1)],
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'CELLS %i %i'%(N,N*9),
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]
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# cells
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for i in range (res[2]):
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for j in range (res[1]):
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for k in range (res[0]):
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base = i*(res[1]+1)*(res[2]+1)+j*(res[1]+1)+k
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cmds.append('8 '+'\t'.join(map(str,[ \
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base,
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base+1,
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base+res[1]+2,
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base+res[1]+1,
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base+(res[1]+1)*(res[2]+1),
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base+(res[1]+1)*(res[2]+1)+1,
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base+(res[1]+1)*(res[2]+1)+res[1]+2,
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base+(res[1]+1)*(res[2]+1)+res[1]+1,
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])))
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cmds += [\
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'CELL_TYPES %i'%N,
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['12']*N,
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'CELL_DATA %i'%N,
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]
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for type in data:
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for item in data[type]:
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print type,item
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cmds += [\
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'%s %s float'%(type.upper(),item),
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'LOOKUP_TABLE default',
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[[['\t'.join(map(str,data[type][item][:,j,k]))] for j in range(res[1])] for k in range(res[2])],
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]
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# vtk = open(filename, 'w')
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# output(cmd,{'filepointer':vtk},'File')
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# vtk.close()
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return cmds
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# +++++++++++++++++++++++++++++++++++++++++++++++++++
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def vtk_writeASCII_points(coordinates,data,res):
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# +++++++++++++++++++++++++++++++++++++++++++++++++++
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""" function writes data array defined on a point field """
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N = res[0]*res[1]*res[2]
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cmds = [\
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'# vtk DataFile Version 3.1',
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'powered by 3Dvisualize',
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'ASCII',
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'DATASET UNSTRUCTURED_GRID',
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'POINTS %i float'%N,
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[[['\t'.join(map(str,coordinates[i,j,k])) for i in range(res[0])] for j in range(res[1])] for k in range(res[2])],
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'CELLS %i %i'%(N,N*2),
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['1\t%i'%i for i in range(N)],
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'CELL_TYPES %i'%N,
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['1']*N,
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'POINT_DATA %i'%N,
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]
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for type in data:
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for item in data[type]:
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cmds += [\
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'%s %s float'%(type.upper(),item),
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'LOOKUP_TABLE default',
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[[['\t'.join(map(str,data[type][item][:,j,k]))] for j in range(res[1])] for k in range(res[2])]
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]
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return cmds
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# +++++++++++++++++++++++++++++++++++++++++++++++++++++
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def vtk_writeASCII_box(diag,defgrad):
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# +++++++++++++++++++++++++++++++++++++++++++++++++++++
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""" corner box for the average defgrad """
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points = numpy.array([\
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[0.0,0.0,0.0,],\
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[diag[0],0.0,0.0,],\
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[diag[0],diag[1],0.0,],\
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[0.0,diag[1],0.0,],\
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[0.0,0.0,diag[2],],\
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[diag[0],0.0,diag[2],],\
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[diag[0],diag[1],diag[2],],\
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[0.0,diag[1],diag[2],],\
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])
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cmds = [\
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'# vtk DataFile Version 3.1',
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'powered by 3Dvisualize',
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'ASCII',
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'DATASET UNSTRUCTURED_GRID',
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'POINTS 8 float',
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['\t'.join(map(str,numpy.dot(defgrad_av,points[p]))) for p in range(8)],
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'CELLS 8 16',
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['1\t%i'%i for i in range(8)],
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'CELL_TYPES 8',
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['1']*8,
|
||||||
|
]
|
||||||
|
|
||||||
|
return cmds
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
# ----------------------- MAIN -------------------------------
|
||||||
|
|
||||||
|
parser = OptionParser(option_class=extendedOption, usage='%prog [options] datafile', description = """
|
||||||
|
Produce VTK file from data field.
|
||||||
|
|
||||||
|
$Id$
|
||||||
|
""")
|
||||||
|
parser.add_option('-s', '--scalar', action='extend', dest='scalar', type='string', \
|
||||||
|
help='list of scalars to visualize')
|
||||||
|
parser.add_option('-d', '--deformation', dest='defgrad', type='string', \
|
||||||
|
help='heading of deformation gradient columns [%default]')
|
||||||
|
parser.add_option('-g', '--grain', dest='grain', type='int', \
|
||||||
|
help='grain of interest [%default]')
|
||||||
|
|
||||||
|
parser.set_defaults(defgrad = 'f')
|
||||||
|
parser.set_defaults(grain = 1)
|
||||||
|
parser.set_defaults(scalar = [])
|
||||||
|
parser.set_defaults(vector = [])
|
||||||
|
parser.set_defaults(tensor = [])
|
||||||
|
|
||||||
|
(options, args) = parser.parse_args()
|
||||||
|
|
||||||
|
for filename in args:
|
||||||
|
if not os.path.exists(filename):
|
||||||
|
continue
|
||||||
|
file = open(filename)
|
||||||
|
content = file.readlines()
|
||||||
|
file.close()
|
||||||
|
m = re.search('(\d+)\shead',content[0],re.I)
|
||||||
|
if m == None:
|
||||||
|
continue
|
||||||
|
print filename
|
||||||
|
|
||||||
|
headrow = int(m.group(1))
|
||||||
|
headings = content[headrow].split()
|
||||||
|
column = {}
|
||||||
|
maxcol = 0
|
||||||
|
|
||||||
|
for col,head in enumerate(headings):
|
||||||
|
if head == 'ip.x':
|
||||||
|
ipcol = col
|
||||||
|
maxcol = max(maxcol,col+3)
|
||||||
|
break
|
||||||
|
|
||||||
|
if ipcol < 0:
|
||||||
|
print 'missing ip coordinates..!'
|
||||||
|
continue
|
||||||
|
|
||||||
|
column['tensor'] = {}
|
||||||
|
for label in [options.defgrad] + options.tensor:
|
||||||
|
column['tensor'][label] = -1
|
||||||
|
for col,head in enumerate(headings):
|
||||||
|
if head == label or head == '%i_1_%s'%(options.grain,label):
|
||||||
|
column['tensor'][label] = col
|
||||||
|
maxcol = max(maxcol,col+9)
|
||||||
|
break
|
||||||
|
|
||||||
|
if column['tensor'][options.defgrad] < 0:
|
||||||
|
print 'missing deformation gradient..!'
|
||||||
|
continue
|
||||||
|
|
||||||
|
column['vector'] = {}
|
||||||
|
for label in options.vector:
|
||||||
|
column['vector'][label] = -1
|
||||||
|
for col,head in enumerate(headings):
|
||||||
|
if head == label or head == '%i_1_%s'%(options.grain,label):
|
||||||
|
column['vector'][label] = col
|
||||||
|
maxcol = max(maxcol,col+3)
|
||||||
|
break
|
||||||
|
|
||||||
|
column['scalar'] = {}
|
||||||
|
for label in options.scalar:
|
||||||
|
column['scalar'][label] = -1
|
||||||
|
for col,head in enumerate(headings):
|
||||||
|
if head == label or head == '%i_%s'%(options.grain,label):
|
||||||
|
column['scalar'][label] = col
|
||||||
|
maxcol = max(maxcol,col+1)
|
||||||
|
break
|
||||||
|
|
||||||
|
values = numpy.array([map(float,line.split()[:maxcol]) for line in content[headrow+1:]],'d')
|
||||||
|
N = len(values)
|
||||||
|
grid = [{},{},{}]
|
||||||
|
for i in range(N):
|
||||||
|
grid[0][str(values[i,ipcol+0])] = True
|
||||||
|
grid[1][str(values[i,ipcol+1])] = True
|
||||||
|
grid[2][str(values[i,ipcol+2])] = True
|
||||||
|
|
||||||
|
res = numpy.array([len(grid[0]),\
|
||||||
|
len(grid[1]),\
|
||||||
|
len(grid[2]),],'i')
|
||||||
|
dim = numpy.array([max(map(float,grid[0].keys()))-min(map(float,grid[0].keys())),\
|
||||||
|
max(map(float,grid[1].keys()))-min(map(float,grid[1].keys())),\
|
||||||
|
max(map(float,grid[1].keys()))-min(map(float,grid[1].keys())),]*res/(res-numpy.ones(3)), 'd')
|
||||||
|
|
||||||
|
print 'resolution',res
|
||||||
|
print 'dimension',dim
|
||||||
|
|
||||||
|
(centroids, defgrad_av) = deformed(res,dim,
|
||||||
|
numpy.reshape(values[:,column['tensor'][options.defgrad]:
|
||||||
|
column['tensor'][options.defgrad]+9],
|
||||||
|
(res[0],res[1],res[2],3,3)))
|
||||||
|
ms = mesh(res,dim,defgrad_av,centroids)
|
||||||
|
|
||||||
|
fields = {\
|
||||||
|
'tensors': {},\
|
||||||
|
'vectors': {},\
|
||||||
|
'scalars': {},\
|
||||||
|
}
|
||||||
|
for me in options.tensor:
|
||||||
|
fields['tensors'][me] = numpy.reshape(values[:,column['tensor'][me]:column['tensor'][me]+9],(res[0],res[1],res[2],3,3))
|
||||||
|
print me,fields['tensors'][me].shape
|
||||||
|
for me in options.vector:
|
||||||
|
fields['vectors'][me] = numpy.reshape(values[:,column['vector'][me]:column['vector'][me]+3],(res[0],res[1],res[2],3))
|
||||||
|
print me,fields['vectors'][me].shape
|
||||||
|
for me in options.scalar:
|
||||||
|
fields['scalars'][me] = numpy.reshape(values[:,column['scalar'][me]],(res[0],res[1],res[2]))
|
||||||
|
print me,fields['scalars'][me].shape
|
||||||
|
|
||||||
|
out = {}
|
||||||
|
out['mesh'] = vtk_writeASCII_mesh(ms,fields,res)
|
||||||
|
out['points'] = vtk_writeASCII_points(centroids,fields,res)
|
||||||
|
out['box'] = vtk_writeASCII_box(dim,defgrad_av)
|
||||||
|
|
||||||
|
for what in out.keys():
|
||||||
|
vtk = open(os.path.splitext(filename)[0]+'_%s.vtk'%what, 'w')
|
||||||
|
output(out[what],{'filepointer':vtk},'File')
|
||||||
|
vtk.close()
|
||||||
Loading…
Reference in New Issue