557 lines
21 KiB
Python
Executable File
557 lines
21 KiB
Python
Executable File
#!/usr/bin/env python
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# -*- coding: UTF-8 no BOM -*-
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import os,sys,threading,re,time,string,fnmatch,vtk
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import numpy as np
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from optparse import OptionParser
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from vtk.util import numpy_support
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import damask
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scriptID = string.replace('$Id$','\n','\\n')
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scriptName = scriptID.split()[1]
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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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def transliterateToFloat(x):
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try:
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return float(x)
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except:
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return 0.0
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def unravel(item):
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if hasattr(item,'__contains__'): return ' '.join(map(unravel,item))
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else: return str(item)
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# ++++++++++++++++++++++++++++++++++++++++++++++++++++
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def vtk_writeASCII_mesh(mesh,data,res,sep):
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# ++++++++++++++++++++++++++++++++++++++++++++++++++++
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""" function writes data array defined on a hexahedral mesh (geometry) """
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info = {\
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'tensor': {'name':'tensor','len':9},\
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'vector': {'name':'vector','len':3},\
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'scalar': {'name':'scalar','len':1},\
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'double': {'name':'scalar','len':2},\
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'triple': {'name':'scalar','len':3},\
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'quadruple': {'name':'scalar','len':4},\
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}
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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 %s'%scriptID,
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'ASCII',
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'DATASET UNSTRUCTURED_GRID',
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'POINTS %i double'%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 z in range (res[2]):
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for y in range (res[1]):
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for x in range (res[0]):
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base = z*(res[1]+1)*(res[0]+1)+y*(res[0]+1)+x
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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[0]+2,
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base+res[0]+1,
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base+(res[1]+1)*(res[0]+1),
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base+(res[1]+1)*(res[0]+1)+1,
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base+(res[1]+1)*(res[0]+1)+res[0]+2,
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base+(res[1]+1)*(res[0]+1)+res[0]+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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plural = {True:'',False:'S'}[type.lower().endswith('s')]
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for item in data[type]['_order_']:
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cmds += [\
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'%s %s double %i'%(info[type]['name'].upper()+plural,item,info[type]['len']),
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{True:'LOOKUP_TABLE default',False:''}[info[type]['name'][:3]=='sca'],
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[[[sep.join(map(unravel,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 gmsh_writeASCII_mesh(mesh,data,res,sep):
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# ++++++++++++++++++++++++++++++++++++++++++++++++++++
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""" function writes data array defined on a hexahedral mesh (geometry) """
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info = {\
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'tensor': {'name':'tensor','len':9},\
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'vector': {'name':'vector','len':3},\
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'scalar': {'name':'scalar','len':1},\
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'double': {'name':'scalar','len':2},\
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'triple': {'name':'scalar','len':3},\
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'quadruple': {'name':'scalar','len':4},\
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}
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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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'$MeshFormat',
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'2.1 0 8',
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'$EndMeshFormat',
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'$Nodes',
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'%i float'%N1,
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[[['\t'.join(map(str,l,mesh[:,i,j,k])) for l in range(1,N1+1) for i in range(res[0]+1)] for j in range(res[1]+1)] for k in range(res[2]+1)],
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'$EndNodes',
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'$Elements',
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'%i'%N,
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]
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# cells
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n_elem = 0
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for z in range (res[2]):
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for y in range (res[1]):
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for x in range (res[0]):
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base = z*(res[1]+1)*(res[0]+1)+y*(res[0]+1)+x
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n_elem +=1
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cmds.append('\t'.join(map(str,[ \
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n_elem,
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'5',
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base,
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base+1,
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base+res[0]+2,
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base+res[0]+1,
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base+(res[1]+1)*(res[0]+1),
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base+(res[1]+1)*(res[0]+1)+1,
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base+(res[1]+1)*(res[0]+1)+res[0]+2,
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base+(res[1]+1)*(res[0]+1)+res[0]+1,
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])))
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cmds += [\
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'ElementData',
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'1',
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'%s'%item, # name of the view
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'0.0', # thats the time value
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'3',
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'0', # time step
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'1',
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'%i'%N
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]
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for type in data:
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plural = {True:'',False:'S'}[type.lower().endswith('s')]
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for item in data[type]['_order_']:
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cmds += [\
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'%s %s float %i'%(info[type]['name'].upper()+plural,item,info[type]['len']),
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'LOOKUP_TABLE default',
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[[[sep.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_points(coordinates,data,res,sep):
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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 %s'%scriptID,
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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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plural = {True:'',False:'S'}[type.lower().endswith('s')]
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for item in data[type]:
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cmds += [\
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'%s %s float'%(type.upper()+plural,item),
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{True:'LOOKUP_TABLE default',False:''}[type.lower()[:3]=='sca'],
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[[[sep.join(map(unravel,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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# ----------------------- MAIN -------------------------------
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parser = OptionParser(option_class=damask.extendableOption, usage='%prog [options] datafile[s]', description = """
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Produce VTK file from data field.
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Coordinates are taken from (consecutive) x, y, and z columns.
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""", version = scriptID)
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sepChoices = ['n','t','s']
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parser.add_option('-s', '--scalar', dest='scalar', action='extend', type='string', metavar = '<string LIST>',
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help='list of single scalars to visualize')
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parser.add_option( '--double', dest='double', action='extend', type='string', metavar = '<string LIST>',
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help='list of two scalars to visualize')
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parser.add_option( '--triple', dest='triple', action='extend', type='string', metavar = '<string LIST>',
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help='list of three scalars to visualize')
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parser.add_option( '--quadruple', dest='quadruple', action='extend', type='string', metavar = '<string LIST>',
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help='list of four scalars to visualize')
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parser.add_option('-v', '--vector', dest='vector', action='extend', type='string', metavar = '<string LIST>',
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help='list of vectors to visualize')
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parser.add_option('-t', '--tensor', dest='tensor', action='extend', type='string', metavar = '<string LIST>',
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help='list of tensors to visualize')
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parser.add_option('-d', '--deformation', dest='defgrad', action='store', type='string', metavar = 'string',
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help='heading of deformation gradient columns [%default]')
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parser.add_option('--reference', dest='undeformed', action='store_true',
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help='map results to reference (undeformed) configuration [%default]')
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parser.add_option('-c','--cell', dest='cell', action='store_true',
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help='data is cell-centered [%default]')
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parser.add_option('-p','--vertex', dest='cell', action='store_false',
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help='data is vertex-centered')
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parser.add_option('--mesh', dest='output_mesh', action='store_true',
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help='produce VTK mesh file [%default]')
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parser.add_option('--nomesh', dest='output_mesh', action='store_false',
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help='omit VTK mesh file')
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parser.add_option('--points', dest='output_points', action='store_true',
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help='produce VTK points file [%default]')
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parser.add_option('--nopoints', dest='output_points', action='store_false',
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help='omit VTK points file')
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parser.add_option('--separator', dest='separator', action='store', type='choice', choices=sepChoices, metavar='string',
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help='data separator (%s) [t]'%(','.join(map(str,sepChoices))))
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parser.add_option('--scaling', dest='scaling', action='extend', type='string',
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help='scaling of fluctuation', metavar = '<float LIST>')
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parser.add_option('-u', '--unitlength', dest='unitlength', action='store', type='float', metavar = 'float',
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help='set unit length for 2D model [%default]')
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parser.add_option('--filenodalcoords', dest='filenodalcoords', action='store', type='string', metavar = 'string',
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help='ASCII table containing nodal coords')
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parser.add_option('--labelnodalcoords', dest='labelnodalcoords', action='store', type='string', nargs=3,
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help='labels of nodal coords in ASCII table %default', metavar = 'string string string')
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parser.add_option('-l', '--linear', dest='linearreconstruction', action='store_true',
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help='use linear reconstruction of geometry [%default]')
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parser.set_defaults(defgrad = 'f')
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parser.set_defaults(separator = 't')
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parser.set_defaults(scalar = [])
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parser.set_defaults(double = [])
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parser.set_defaults(triple = [])
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parser.set_defaults(quadruple = [])
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parser.set_defaults(vector = [])
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parser.set_defaults(tensor = [])
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parser.set_defaults(output_mesh = True)
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parser.set_defaults(output_points = False)
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parser.set_defaults(scaling = [])
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parser.set_defaults(undeformed = False)
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parser.set_defaults(unitlength = 0.0)
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parser.set_defaults(cell = True)
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parser.set_defaults(filenodalcoords = '')
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parser.set_defaults(labelnodalcoords = ['coord.x','coord.y','coord.z'])
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parser.set_defaults(linearreconstruction = False)
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sep = {'n': '\n', 't': '\t', 's': ' '}
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(options, args) = parser.parse_args()
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options.scaling += [1.0 for i in xrange(max(0,3-len(options.scaling)))]
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options.scaling = map(float, options.scaling)
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if np.any(options.scaling != 1.0) and options.linearreconstruction: print 'cannot scale for linear reconstruction'
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if np.any(options.scaling != 1.0) and options.filenodalcoords != '': print 'cannot scale when reading coordinate from file'
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for filename in args:
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if not os.path.exists(filename):
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continue
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file = open(filename)
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content = file.readlines()
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file.close()
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m = re.search('(\d+)\s*head', content[0].lower())
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if m == None:
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continue
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print filename,'\n'
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sys.stdout.flush()
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headrow = int(m.group(1))
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headings = content[headrow].split()
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column = {}
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matches = {}
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maxcol = 0
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locol = -1
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for col,head in enumerate(headings):
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if head == {True:'ip.x',False:'node.x'}[options.cell]:
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locol = col
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maxcol = max(maxcol,col+3)
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break
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if locol < 0:
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print 'missing coordinates..!'
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continue
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column['tensor'] = {}
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matches['tensor'] = {}
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for label in [options.defgrad] + options.tensor:
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column['tensor'][label] = -1
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for col,head in enumerate(headings):
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if head == label or head == '1_'+label:
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column['tensor'][label] = col
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maxcol = max(maxcol,col+9)
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matches['tensor'][label] = [label]
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break
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if not options.undeformed and column['tensor'][options.defgrad] < 0:
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print 'missing deformation gradient "%s"..!'%options.defgrad
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continue
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column['vector'] = {}
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matches['tensor'] = {}
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for label in options.vector:
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column['vector'][label] = -1
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for col,head in enumerate(headings):
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if head == label or head == '1_'+label:
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column['vector'][label] = col
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maxcol = max(maxcol,col+3)
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matches['vector'][label] = [label]
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break
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for length,what in enumerate(['scalar','double','triple','quadruple']):
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column[what] = {}
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labels = eval("options.%s"%what)
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matches[what] = {}
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for col,head in enumerate(headings):
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for needle in labels:
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if fnmatch.fnmatch(head,needle):
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column[what][head] = col
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maxcol = max(maxcol,col+1+length)
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if needle not in matches[what]:
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matches[what][needle] = [head]
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else:
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matches[what][needle] += [head]
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values = np.array(sorted([map(transliterateToFloat,line.split()[:maxcol]) for line in content[headrow+1:]],
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key=lambda x:(x[locol+0],x[locol+1],x[locol+2])),'d') # sort with z as fastest and x as slowest index
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N = len(values)
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tempGrid = [{},{},{}]
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for j in xrange(3):
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for i in xrange(N):
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tempGrid[j][str(values[i,locol+j])] = True
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grid = np.array([len(tempGrid[0]),\
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len(tempGrid[1]),\
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len(tempGrid[2]),],'i')
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dim = np.ones(3)
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for i,r in enumerate(grid):
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if r > 1:
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dim[i] = (max(map(float,tempGrid[i].keys()))-min(map(float,tempGrid[i].keys())))*r/(r-1.0)
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if grid[2]==1: # for 2D case set undefined dimension to given unitlength or alternatively give it the length of the smallest element
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if options.unitlength == 0.0:
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dim[2] = min(dim/grid)
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else:
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dim[2] = options.unitlength
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print dim
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if options.undeformed:
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Favg = np.eye(3)
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else:
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Favg = damask.core.math.tensorAvg(
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np.reshape(np.transpose(values[:,column['tensor'][options.defgrad]:
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column['tensor'][options.defgrad]+9]),
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(3,3,grid[0],grid[1],grid[2])))
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if not options.filenodalcoords:
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F = np.reshape(np.transpose(values[:,column['tensor'][options.defgrad]:
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column['tensor'][options.defgrad]+9]),
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(3,3,grid[0],grid[1],grid[2]))
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if options.linearreconstruction:
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centroids = damask.core.mesh.deformedCoordsLinear(dim,F,Favg)
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else:
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centroids = damask.core.mesh.deformedCoordsFFT(dim,F,Favg,options.scaling)
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nodes = damask.core.mesh.nodesAroundCentres(dim,Favg,centroids)
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else:
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nodes = np.zeros(((3,grid[0]+1)*(grid[1]+1)*(grid[2]+1)),'d')
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filenodalcoords = open(options.filenodalcoords)
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tablenodalcoords = damask.ASCIItable(filenodalcoords)
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tablenodalcoords.head_read()
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columns = [tablenodalcoords.labels.index(options.labelnodalcoords[0]),
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|
tablenodalcoords.labels.index(options.labelnodalcoords[1]),
|
|
tablenodalcoords.labels.index(options.labelnodalcoords[2])]
|
|
i = 0
|
|
while tablenodalcoords.data_read(): # read next data line of ASCII table
|
|
nodes[i,:]=float(tablenodalcoords.data[column[:]])
|
|
i += 1
|
|
|
|
nodes=nodes.reshape(3,grid[0]+1,grid[1]+1,grid[2]+1)
|
|
|
|
#--- generate grid --------------------------------------------------------------------------------
|
|
# structure = vtk.vtkIntArray()
|
|
# structure.SetName('Microstructures')
|
|
# temp = []
|
|
# i=0
|
|
# aHexahedronGrid = vtk.vtkUnstructuredGrid()
|
|
# for z in range (grid[2]):
|
|
# for y in range (grid[1]):
|
|
# for x in range (grid[0]):
|
|
# temp.append(vtk.vtkHexahedron())
|
|
# base = z*(grid[1]+1)*(grid[0]+1)+y*(grid[0]+1)+x
|
|
# temp[i].GetPointIds().SetId(0, base)
|
|
# temp[i].GetPointIds().SetId(1, base+1)
|
|
# temp[i].GetPointIds().SetId(2, base+grid[0]+2)
|
|
# temp[i].GetPointIds().SetId(3, base+grid[0]+1)
|
|
# temp[i].GetPointIds().SetId(4, base+(grid[1]+1)*(grid[0]+1))
|
|
# temp[i].GetPointIds().SetId(5, base+(grid[1]+1)*(grid[0]+1)+1)
|
|
# temp[i].GetPointIds().SetId(6, base+(grid[1]+1)*(grid[0]+1)+grid[0]+2)
|
|
# temp[i].GetPointIds().SetId(7, base+(grid[1]+1)*(grid[0]+1)+grid[0]+1)
|
|
# aHexahedronGrid.InsertNextCell(temp[i].GetCellType(),temp[i].GetPointIds())
|
|
# i+=1
|
|
# structure.InsertNextValue(i)
|
|
|
|
# pcoords = vtk.vtkDoubleArray()
|
|
# pcoords.SetNumberOfComponents(3)
|
|
# for i in range(grid[0]+1):
|
|
# for j in range(grid[1]+1):
|
|
# for k in range(grid[2]+1):
|
|
# pcoords.InsertNextTuple3(nodes[0,i,j,k],nodes[1,i,j,k],nodes[2,i,j,k])
|
|
|
|
# points = vtk.vtkPoints()
|
|
# points.SetData(pcoords)
|
|
# aHexahedronGrid.SetPoints(points)
|
|
# aHexahedronGrid.GetCellData().SetScalars(structure)
|
|
|
|
# outWriter = vtk.vtkXMLUnstructuredGridWriter()
|
|
# outWriter.SetDataModeToBinary()
|
|
# outWriter.SetCompressorTypeToZLib()
|
|
# outWriter.SetFileName('ddd.vtu')
|
|
# outWriter.SetInput(aHexahedronGrid)
|
|
# outWriter.Write()
|
|
|
|
|
|
fields = {\
|
|
'tensor': {},\
|
|
'vector': {},\
|
|
'scalar': {},\
|
|
'double': {},\
|
|
'triple': {},\
|
|
'quadruple': {},\
|
|
}
|
|
reshape = {\
|
|
'tensor': [3,3],\
|
|
'vector': [3],\
|
|
'scalar': [],\
|
|
'double': [2],\
|
|
'triple': [3],\
|
|
'quadruple': [4],\
|
|
}
|
|
length = {\
|
|
'tensor': 9,\
|
|
'vector': 3,\
|
|
'scalar': 1,\
|
|
'double': 2,\
|
|
'triple': 3,\
|
|
'quadruple': 4,\
|
|
}
|
|
|
|
structure = vtk.vtkIntArray()
|
|
structure.SetName('Microstructures')
|
|
for datatype in fields.keys():
|
|
print '\n%s:'%datatype,
|
|
fields[datatype]['_order_'] = []
|
|
for what in eval('options.'+datatype):
|
|
for label in matches[datatype][what]:
|
|
col = column[datatype][label]
|
|
if col != -1:
|
|
print label,
|
|
fields[datatype][label] = np.reshape(values[:,col:col+length[datatype]],[grid[0],grid[1],grid[2]]+reshape[datatype])
|
|
fields[datatype]['_order_'] += [label]
|
|
print '\n'
|
|
|
|
out = {}
|
|
if options.output_mesh: out['mesh'] = vtk_writeASCII_mesh(nodes,fields,grid,sep[options.separator])
|
|
if options.output_points: out['points'] = vtk_writeASCII_points(centroids,fields,grid,sep[options.separator])
|
|
|
|
for what in out.keys():
|
|
print what
|
|
(head,tail) = os.path.split(filename)
|
|
vtk = open(os.path.join(head,what+'_'+os.path.splitext(tail)[0]+'.vtk'), 'w')
|
|
output(out[what],{'filepointer':vtk},'File')
|
|
vtk.close()
|
|
print
|
|
|