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DAMASK_EICMD
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DAMASK_EICMD/processing/post/3Dvisualize

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#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
# This script is used for the post processing of the results achieved by the spectral method.
# As it reads in the data coming from "materialpoint_results", it can be adopted to the data
# computed using the FEM solvers. Until now, its capable to handle elements with one IP in a regular order
# written by M. Diehl, m.diehl@mpie.de
import os,sys,threading,re,numpy,time
from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
# -----------------------------
class extendedOption(Option):
# -----------------------------
# used for definition of new option parser action 'extend', which enables to take multiple option arguments
# taken from online tutorial http://docs.python.org/library/optparse.html
ACTIONS = Option.ACTIONS + ("extend",)
STORE_ACTIONS = Option.STORE_ACTIONS + ("extend",)
TYPED_ACTIONS = Option.TYPED_ACTIONS + ("extend",)
ALWAYS_TYPED_ACTIONS = Option.ALWAYS_TYPED_ACTIONS + ("extend",)
def take_action(self, action, dest, opt, value, values, parser):
if action == "extend":
lvalue = value.split(",")
values.ensure_value(dest, []).extend(lvalue)
else:
Option.take_action(self, action, dest, opt, value, values, parser)
# -----------------------------
class backgroundMessage(threading.Thread):
# -----------------------------
def __init__(self):
threading.Thread.__init__(self)
self.message = ''
self.new_message = ''
self.counter = 0
self.symbols = ['- ', '\ ', '| ', '/ ']
self.waittime = 0.5
def __quit__(self):
length = len(self.message) + len(self.symbols[self.counter])
sys.stderr.write(chr(8)*length + ' '*length + chr(8)*length)
sys.stderr.write('')
def run(self):
while not threading.enumerate()[0]._Thread__stopped:
time.sleep(self.waittime)
self.update_message()
self.__quit__()
def set_message(self, new_message):
self.new_message = new_message
self.print_message()
def print_message(self):
length = len(self.message) + len(self.symbols[self.counter])
sys.stderr.write(chr(8)*length + ' '*length + chr(8)*length) # delete former message
sys.stderr.write(self.symbols[self.counter] + self.new_message) # print new message
self.message = self.new_message
def update_message(self):
self.counter = (self.counter + 1)%len(self.symbols)
self.print_message()
def outStdout(cmd,locals):
if cmd[0:3] == '(!)':
exec(cmd[3:])
elif cmd[0:3] == '(?)':
cmd = eval(cmd[3:])
print cmd
else:
print cmd
return
def outFile(cmd,locals):
if cmd[0:3] == '(!)':
exec(cmd[3:])
elif cmd[0:3] == '(?)':
cmd = eval(cmd[3:])
locals['filepointer'].write(cmd+'\n')
else:
locals['filepointer'].write(cmd+'\n')
return
def output(cmds,locals,dest):
for cmd in cmds:
if isinstance(cmd,list):
output(cmd,locals,dest)
else:
{\
'File': outFile,\
'Stdout': outStdout,\
}[dest](str(cmd),locals)
return
#+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
def mesh(res,geomdim,defgrad_av,centroids):
#+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
neighbor = numpy.array([[0, 0, 0],
[1, 0, 0],
[1, 1, 0],
[0, 1, 0],
[0, 0, 1],
[1, 0, 1],
[1, 1, 1],
[0, 1, 1]])
wrappedCentroids = numpy.zeros([res[0]+2,res[1]+2,res[2]+2,3],'d')
nodes = numpy.zeros([res[0]+1,res[1]+1,res[2]+1,3],'d')
wrappedCentroids[1:-1,1:-1,1:-1] = centroids
diag = numpy.ones(3,'i')
shift = numpy.zeros(3,'i')
lookup = numpy.zeros(3,'i')
for k in range(res[2]+2):
for j in range(res[1]+2):
for i in range(res[0]+2):
if (k==0 or k==res[2]+1 or \
j==0 or j==res[1]+1 or \
i==0 or i==res[0]+1 ):
me = numpy.array([i,j,k],'i')
shift = numpy.sign(res+diag-2*me)*(numpy.abs(res+diag-2*me)/(res+diag))
lookup = me-diag+shift*res
wrappedCentroids[i,j,k] = centroids[lookup[0],lookup[1],lookup[2]]- \
numpy.dot(defgrad_av, shift*geomdim)
for k in range(res[2]+1):
for j in range(res[1]+1):
for i in range(res[0]+1):
for n in range(8):
nodes[i,j,k] += wrappedCentroids[i+neighbor[n,0],j+neighbor[n,1],k+neighbor[n,2]]
nodes[:,:,:] /= 8.0
return nodes
# +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
def deformed(res,geomdimension,defgrad):
# +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
corner = numpy.array([[0, 0, 0],
[1, 0, 0],
[1, 1, 0],
[0, 1, 0],
[1, 1, 1],
[0, 1, 1],
[0, 0, 1],
[1, 0, 1]])
step = numpy.array([[ 1, 1, 1],
[-1, 1, 1],
[-1,-1, 1],
[ 1,-1, 1],
[-1,-1,-1],
[ 1,-1,-1],
[ 1, 1,-1],
[-1, 1,-1]])
order = numpy.array([[0, 1, 2],
[0, 2, 1],
[1, 0, 2],
[1, 2, 0],
[2, 0, 1],
[2, 1, 0]])
coord = numpy.zeros([8,6,res[0],res[1],res[2],3], 'd')
coord_avgOrder = numpy.zeros([8,res[0],res[1],res[2],3], 'd')
coord_avgCorner = numpy.zeros([res[0],res[1],res[2],3], 'd')
myStep = numpy.zeros(3,'d')
rear = numpy.zeros(3,'i')
init = numpy.zeros(3,'i')
oppo = numpy.zeros(3,'i')
me = numpy.zeros(3,'i')
ones = numpy.ones( 3,'i')
fones = numpy.ones( 3,'d')
defgrad_av=numpy.average(numpy.average(numpy.average(defgrad,0),0),0)
for s in range(8): # corners
init = corner[s]*(res-ones)
oppo = corner[(s+4)%8]*(res-ones)
sys.stdout.write('.'*(8-s)+' '*s+'\r')
sys.stdout.flush()
for o in range(6): # orders
for k in range(init[order[o,2]],oppo[order[o,2]]+step[s,order[o,2]],step[s,order[o,2]]):
rear[order[o,1]] = init[order[o,1]]
for j in range(init[order[o,1]],oppo[order[o,1]]+step[s,order[o,1]],step[s,order[o,1]]):
rear[order[o,0]] = init[order[o,0]]
for i in range(init[order[o,0]],oppo[order[o,0]]+step[s,order[o,0]],step[s,order[o,0]]):
me[order[o,0]] = i
me[order[o,1]] = j
me[order[o,2]] = k
if (numpy.all(me == init)):
coord[s,o,me[0],me[1],me[2]] = geomdimension * (numpy.dot(defgrad_av,corner[s]) + \
numpy.dot(defgrad[me[0],me[1],me[2]],0.5*step[s]/res))
else:
myStep = (me-rear)*geomdimension/res
coord[s,o,me[0],me[1],me[2]] = coord[s,o,rear[0],rear[1],rear[2]] + \
0.5*numpy.dot(defgrad[me[0],me[1],me[2]] + \
defgrad[rear[0],rear[1],rear[2]],myStep)
rear[:] = me[:]
coord_avgOrder[s] = numpy.average(coord[s],0)
for k in range(res[2]):
for j in range(res[1]):
for i in range(res[0]):
parameter_coords = (2.0*numpy.array([i,j,k])-res+fones)/(res-fones)
pos = fones + parameter_coords
neg = fones - parameter_coords
coord_avgCorner[i,j,k] = ( coord_avgOrder[0,i,j,k] *neg[0]*neg[1]*neg[2]\
+ coord_avgOrder[1,i,j,k] *pos[0]*neg[1]*neg[2]\
+ coord_avgOrder[2,i,j,k] *pos[0]*pos[1]*neg[2]\
+ coord_avgOrder[3,i,j,k] *neg[0]*pos[1]*neg[2]\
+ coord_avgOrder[4,i,j,k] *pos[0]*pos[1]*pos[2]\
+ coord_avgOrder[5,i,j,k] *neg[0]*pos[1]*pos[2]\
+ coord_avgOrder[6,i,j,k] *neg[0]*neg[1]*pos[2]\
+ coord_avgOrder[7,i,j,k] *pos[0]*neg[1]*pos[2])*0.125
print ' '
return coord_avgCorner, defgrad_av
# ++++++++++++++++++++++++++++++++++++++++++++++++++++
def vtk_writeASCII_mesh(mesh,data,res):
# ++++++++++++++++++++++++++++++++++++++++++++++++++++
""" function writes data array defined on a hexahedral mesh (geometry) """
N1 = (res[0]+1)*(res[1]+1)*(res[2]+1)
N = res[0]*res[1]*res[2]
cmds = [\
'# vtk DataFile Version 3.1',
'powered by 3Dvisualize',
'ASCII',
'DATASET UNSTRUCTURED_GRID',
'POINTS %i float'%N1,
[[['\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)],
'CELLS %i %i'%(N,N*9),
]
# cells
for i in range (res[2]):
for j in range (res[1]):
for k in range (res[0]):
base = i*(res[1]+1)*(res[2]+1)+j*(res[1]+1)+k
cmds.append('8 '+'\t'.join(map(str,[ \
base,
base+1,
base+res[1]+2,
base+res[1]+1,
base+(res[1]+1)*(res[2]+1),
base+(res[1]+1)*(res[2]+1)+1,
base+(res[1]+1)*(res[2]+1)+res[1]+2,
base+(res[1]+1)*(res[2]+1)+res[1]+1,
])))
cmds += [\
'CELL_TYPES %i'%N,
['12']*N,
'CELL_DATA %i'%N,
]
for type in data:
for item in data[type]:
print type,item
cmds += [\
'%s %s float'%(type.upper(),item),
'LOOKUP_TABLE default',
[[['\t'.join(map(str,data[type][item][:,j,k]))] for j in range(res[1])] for k in range(res[2])],
]
# vtk = open(filename, 'w')
# output(cmd,{'filepointer':vtk},'File')
# vtk.close()
return cmds
# +++++++++++++++++++++++++++++++++++++++++++++++++++
def vtk_writeASCII_points(coordinates,data,res):
# +++++++++++++++++++++++++++++++++++++++++++++++++++
""" function writes data array defined on a point field """
N = res[0]*res[1]*res[2]
cmds = [\
'# vtk DataFile Version 3.1',
'powered by 3Dvisualize',
'ASCII',
'DATASET UNSTRUCTURED_GRID',
'POINTS %i float'%N,
[[['\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])],
'CELLS %i %i'%(N,N*2),
['1\t%i'%i for i in range(N)],
'CELL_TYPES %i'%N,
['1']*N,
'POINT_DATA %i'%N,
]
for type in data:
for item in data[type]:
cmds += [\
'%s %s float'%(type.upper(),item),
'LOOKUP_TABLE default',
[[['\t'.join(map(str,data[type][item][:,j,k]))] for j in range(res[1])] for k in range(res[2])]
]
return cmds
# +++++++++++++++++++++++++++++++++++++++++++++++++++++
def vtk_writeASCII_box(diag,defgrad):
# +++++++++++++++++++++++++++++++++++++++++++++++++++++
""" corner box for the average defgrad """
points = numpy.array([\
[0.0,0.0,0.0,],\
[diag[0],0.0,0.0,],\
[diag[0],diag[1],0.0,],\
[0.0,diag[1],0.0,],\
[0.0,0.0,diag[2],],\
[diag[0],0.0,diag[2],],\
[diag[0],diag[1],diag[2],],\
[0.0,diag[1],diag[2],],\
])
cmds = [\
'# vtk DataFile Version 3.1',
'powered by 3Dvisualize',
'ASCII',
'DATASET UNSTRUCTURED_GRID',
'POINTS 8 float',
['\t'.join(map(str,numpy.dot(defgrad_av,points[p]))) for p in range(8)],
'CELLS 8 16',
['1\t%i'%i for i in range(8)],
'CELL_TYPES 8',
['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()
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