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,string,postprocessingMath
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 transliterateToFloat(x):
try:
return float(x)
except:
return 0.0
# ++++++++++++++++++++++++++++++++++++++++++++++++++++
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',
string.replace('powered by $Id$','\n','\\n'),
'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 z in range (res[2]):
for y in range (res[1]):
for x in range (res[0]):
base = z*(res[1]+1)*(res[0]+1)+y*(res[0]+1)+x
cmds.append('8 '+'\t'.join(map(str,[ \
base,
base+1,
base+res[0]+2,
base+res[0]+1,
base+(res[1]+1)*(res[0]+1),
base+(res[1]+1)*(res[0]+1)+1,
base+(res[1]+1)*(res[0]+1)+res[0]+2,
base+(res[1]+1)*(res[0]+1)+res[0]+1,
])))
cmds += [\
'CELL_TYPES %i'%N,
['12']*N,
'CELL_DATA %i'%N,
]
for type in data:
plural = {True:'',False:'S'}[type.lower().endswith('s')]
for item in data[type]:
cmds += [\
'%s %s float'%(type.upper()+plural,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 gmsh_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 = [\
'$MeshFormat',
'2.1 0 8',
'$EndMeshFormat',
'$Nodes',
'%i float'%N1,
[[['\t'.join(map(str,l,mesh[i,j,k])) for l in range(1,N1+1) for i in range(res[0]+1)] for j in range(res[1]+1)] for k in range(res[2]+1)],
'$EndNodes',
'$Elements',
'%i'%N,
]
# cells
n_elem = 0
for z in range (res[2]):
for y in range (res[1]):
for x in range (res[0]):
base = z*(res[1]+1)*(res[0]+1)+y*(res[0]+1)+x
n_elem +=1
cmds.append('\t'.join(map(str,[ \
n_elem,
'5',
base,
base+1,
base+res[0]+2,
base+res[0]+1,
base+(res[1]+1)*(res[0]+1),
base+(res[1]+1)*(res[0]+1)+1,
base+(res[1]+1)*(res[0]+1)+res[0]+2,
base+(res[1]+1)*(res[0]+1)+res[0]+1,
])))
cmds += [\
'ElementData',
'1',
'%s'%item, # name of the view
'0.0', # thats the time value
'3',
'0', # time step
'1',
'%i'%N
]
for type in data:
plural = {True:'',False:'S'}[type.lower().endswith('s')]
for item in data[type]:
cmds += [\
'%s %s float'%(type.upper()+plural,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_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 $Id$',
'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:
plural = {True:'',False:'S'}[type.lower().endswith('s')]
for item in data[type]:
cmds += [\
'%s %s float'%(type.upper()+plural,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 $Id$',
'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[s]', description = """
Produce VTK file from data field. Coordinates are taken from (consecutive) ip.x, ip.y, and ip.z columns.
2011-08-18 13:30:19 +05:30
""" + string.replace('$Id$','\n','\\n')
)
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('-m', '--mesh', dest='output_mesh', action='store_true', \
help='produce VTK mesh file [%default]')
parser.add_option('-p', '--points', dest='output_points', action='store_true', \
help='produce VTK points file [%default]')
parser.add_option('-b', '--box', dest='output_box', action='store_true', \
help='produce VTK box file [%default]')
parser.add_option('--scaling', dest='scaling', type='int', nargs=1, \
help='scaling of fluctuastion [%default]')
parser.add_option('--undeformed', dest='undeformed', action='store_true',\
help='do not calculate average deformation of ve [%default]')
parser.set_defaults(defgrad = 'f')
parser.set_defaults(scalar = [])
parser.set_defaults(vector = [])
parser.set_defaults(tensor = [])
parser.set_defaults(output_mesh = True)
parser.set_defaults(output_points = False)
parser.set_defaults(output_box = False)
parser.set_defaults(scaling = 1)
parser.set_defaults(undeformed = False)
(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,
sys.stdout.flush()
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 == '1_%s'%label:
column['tensor'][label] = col
maxcol = max(maxcol,col+9)
break
if column['tensor'][options.defgrad] < 0:
print 'missing deformation gradient "%s"..!'%options.defgrad
continue
column['vector'] = {}
for label in options.vector:
column['vector'][label] = -1
for col,head in enumerate(headings):
if head == label or head == '1_%s'%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:
column['scalar'][label] = col
maxcol = max(maxcol,col+1)
break
values = numpy.array(sorted([map(transliterateToFloat,line.split()[:maxcol]) for line in content[headrow+1:]],
key=lambda x:(x[ipcol+0],x[ipcol+1],x[ipcol+2])), # sort with z as fastest and x as slowest index
'd')
N = len(values)
grid = [{},{},{}]
for j in range(3):
for i in range(N):
grid[j][str(values[i,ipcol+j])] = True
res = numpy.array([len(grid[0]),\
len(grid[1]),\
len(grid[2]),],'i')
dim = numpy.ones(3)
for i,r in enumerate(res):
if r > 1:
dim[i] = (max(map(float,grid[i].keys()))-min(map(float,grid[i].keys())))*r/(r-1.0)
for i,r in enumerate(res): # for 2D (and 1D) case make undefined dimension thin
if r == 1 :
dim[i] = 1.0/float(max(res))*min(dim)
if options.undeformed:
defgrad_av = numpy.array([[1.0,0.0,0.0],[0.0,1.0,0.0],[0.0,0.0,1.0]])
else:
defgrad_av = postprocessingMath.tensor_avg(res[0],res[1],res[2],\
numpy.reshape(values[:,column['tensor'][options.defgrad]:
column['tensor'][options.defgrad]+9],
(res[0],res[1],res[2],3,3)))
centroids = postprocessingMath.deformed_fft(res[0],res[1],res[2],dim,\
numpy.reshape(values[:,column['tensor'][options.defgrad]:
column['tensor'][options.defgrad]+9],
(res[0],res[1],res[2],3,3)),defgrad_av,options.scaling)
ms = postprocessingMath.mesh(res[0],res[1],res[2],dim,defgrad_av,centroids)
fields = {\
'tensor': {},\
'vector': {},\
'scalar': {},\
}
reshape = {\
'tensor': (3,3),\
'vector': (3),\
'scalar': (),\
}
length = {\
'tensor': 9,\
'vector': 3,\
'scalar': 1,\
}
for datatype in fields.keys():
print '\n%s:'%datatype,
for what in eval('options.%s'%datatype):
col = column[datatype][what]
if col != -1:
print what,
fields[datatype][what] = numpy.reshape(values[:,col:col+length[datatype]],(res[0],res[1],res[2])+reshape[datatype])
print '\n'
out = {}
if options.output_mesh: out['mesh'] = vtk_writeASCII_mesh(ms,fields,res)
if options.output_points: out['points'] = vtk_writeASCII_points(centroids,fields,res)
if options.output_box: out['box'] = vtk_writeASCII_box(dim,defgrad_av)
for what in out.keys():
print what
(head,tail) = os.path.split(filename)
vtk = open(os.path.join(head,'%s_'%what+os.path.splitext(tail)[0]+'.vtk'), 'w')
output(out[what],{'filepointer':vtk},'File')
vtk.close()
print