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renamed spectral_buildElements.py to nodesFromCentroids.py and added first simple version of an ascii table to ang converter

This commit is contained in:
Martin Diehl 2012-08-30 17:01:46 +00:00
parent 299d9e6bc4
commit b7dc9f9944
5 changed files with 278 additions and 45 deletions
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50
processing/post/3Dvisualize.py
View File

@ -344,6 +344,10 @@ parser.add_option('--scaling', dest='scaling', type='float', \
help='scaling of fluctuation [%default]') help='scaling of fluctuation [%default]')
parser.add_option('-u', '--unitlength', dest='unitlength', type='float', \ parser.add_option('-u', '--unitlength', dest='unitlength', type='float', \
help='set unit length for 2D model [%default]') help='set unit length for 2D model [%default]')
parser.add_option('--filenodalcoords', dest='filenodalcoords', type='string', \
help='ASCII table containing nodal coords')
parser.add_option('--labelnodalcoords', dest='nodalcoords', type='string', \
help='labels of nodal coords in ASCII table')
parser.add_option('-l', '--linear', dest='linearreconstruction', action='store_true',\ parser.add_option('-l', '--linear', dest='linearreconstruction', action='store_true',\
help='use linear reconstruction of geometry [%default]') help='use linear reconstruction of geometry [%default]')
@ -362,12 +366,15 @@ parser.set_defaults(scaling = 1.0)
parser.set_defaults(undeformed = False) parser.set_defaults(undeformed = False)
parser.set_defaults(unitlength = 0.0) parser.set_defaults(unitlength = 0.0)
parser.set_defaults(cell = True) parser.set_defaults(cell = True)
parser.set_defaults(filenodalcoords = '')
parser.set_defaults(labelnodalcoords = 'coord')
parser.set_defaults(linearreconstruction = False) parser.set_defaults(linearreconstruction = False)
sep = {'n': '\n', 't': '\t', 's': ' '} sep = {'n': '\n', 't': '\t', 's': ' '}
(options, args) = parser.parse_args() (options, args) = parser.parse_args()
if options.scaling !=1.0 and options.linearreconstruction: print 'cannot scale for linear reconstruction'
if options.scaling !=1.0 and options.filenodalcoords!='': print 'cannot scale when reading coordinate from file'
options.separator = options.separator.lower() options.separator = options.separator.lower()
for filename in args: for filename in args:
if not os.path.exists(filename): if not os.path.exists(filename):
@ -453,23 +460,34 @@ for filename in args:
else: else:
dim[2] = options.unitlength dim[2] = options.unitlength
if options.filenodalcoords:
mesh = numpy.zeros(((res[0]+1)*(res[1]+1)*(res[2]+1),3),'d')
mesh=mesh.reshape(res[0]+1,res[1]+1,res[2]+1,3)
filenodalcoords = open(options.filenodalcoords)
tablenodalcoords = damask.ASCIItable(filenodalcoords)
tablenodalcoords.head_read()
coord = tablenodalcoords.labels.index(options.labelnodalcoords+'.x')
i = 0
while tablenodalcoords.data_read():
mesh[i%(res[0]+1),(i//(res[0]+1))%(res[1]+1),(i//(res[0]+1)//(res[1]+1)) % (res[2]+1),:]=\
[float(tablenodalcoords.data[coord]),
float(tablenodalcoords.data[coord+1]),
float(tablenodalcoords.data[coord+2])]
i += 1
else:
F = numpy.reshape(values[:,column['tensor'][options.defgrad]: column['tensor'][options.defgrad]+9],(res[0],res[1],res[2],3,3))
if options.undeformed: if options.undeformed:
defgrad_av = numpy.eye(3) Favg = numpy.eye(3)
else: else:
defgrad_av = damask.core.math.tensorAvg(numpy.reshape(values[:,column['tensor'][options.defgrad]: Favg = damask.core.math.tensorAvg(F)
column['tensor'][options.defgrad]+9],
(res[0],res[1],res[2],3,3)))
if options.linearreconstruction: if options.linearreconstruction:
centroids = damask.core.mesh.deformed_linear(res,dim,defgrad_av, centroids = damask.core.mesh.deformed_linear(res,dim,Favg,F)
numpy.reshape(values[:,column['tensor'][options.defgrad]:
column['tensor'][options.defgrad]+9],
(res[0],res[1],res[2],3,3)))
else: else:
centroids = damask.core.mesh.deformed_fft(res,dim,defgrad_av,options.scaling, centroids = damask.core.mesh.deformed_fft(res,dim,Favg,options.scaling,F)
numpy.reshape(values[:,column['tensor'][options.defgrad]: mesh = damask.core.mesh.mesh_regular_grid(res,dim,Favg,centroids)
column['tensor'][options.defgrad]+9],
(res[0],res[1],res[2],3,3)))
ms = damask.core.mesh.mesh_regular_grid(res,dim,defgrad_av,centroids)
fields = {\ fields = {\
'tensor': {},\ 'tensor': {},\
'vector': {},\ 'vector': {},\
@ -505,9 +523,9 @@ for filename in args:
print '\n' print '\n'
out = {} out = {}
if options.output_mesh: out['mesh'] = vtk_writeASCII_mesh(ms,fields,res,sep[options.separator]) if options.output_mesh: out['mesh'] = vtk_writeASCII_mesh(mesh,fields,res,sep[options.separator])
if options.output_points: out['points'] = vtk_writeASCII_points(centroids,fields,res,sep[options.separator]) if options.output_points: out['points'] = vtk_writeASCII_points(centroids,fields,res,sep[options.separator])
if options.output_box: out['box'] = vtk_writeASCII_box(dim,defgrad_av) if options.output_box: out['box'] = vtk_writeASCII_box(dim,Favg)
for what in out.keys(): for what in out.keys():
print what print what

9
processing/post/addDeformedConfiguration.py
View File

@ -48,9 +48,12 @@ parser.add_option('-c','--coordinates', dest='coords', type='string',\
help='column heading for coordinates [%default]') help='column heading for coordinates [%default]')
parser.add_option('-d','--defgrad', dest='defgrad', type='string', \ parser.add_option('-d','--defgrad', dest='defgrad', type='string', \
help='heading of columns containing tensor field values') help='heading of columns containing tensor field values')
parser.add_option('-l', '--linear', dest='linearreconstruction', action='store_true',\
help='use linear reconstruction of geometry [%default]')
parser.set_defaults(coords = 'ip') parser.set_defaults(coords = 'ip')
parser.set_defaults(defgrad = 'f' ) parser.set_defaults(defgrad = 'f' )
parser.set_defaults(linearreconstruction = False)
(options,filenames) = parser.parse_args() (options,filenames) = parser.parse_args()
@ -115,7 +118,7 @@ for file in files:
sys.stderr.write('column %s not found...\n'%key) sys.stderr.write('column %s not found...\n'%key)
else: else:
defgrad = numpy.array([0.0 for i in xrange(N*9)]).reshape(list(res)+[3,3]) defgrad = numpy.array([0.0 for i in xrange(N*9)]).reshape(list(res)+[3,3])
table.labels_append(['%s_deformed'%(coord) for coord in 'x','y','z']) # extend ASCII header with new labels table.labels_append(['ip_deformed.%s'%(coord) for coord in 'x','y','z']) # extend ASCII header with new labels
column = table.labels.index(key) column = table.labels.index(key)
# ------------------------------------------ assemble header --------------------------------------- # ------------------------------------------ assemble header ---------------------------------------
@ -134,8 +137,10 @@ for file in files:
# ------------------------------------------ process value field ---------------------------- # ------------------------------------------ process value field ----------------------------
defgrad_av = damask.core.math.tensorAvg(defgrad) defgrad_av = damask.core.math.tensorAvg(defgrad)
if options.linearreconstruction:
centroids = damask.core.mesh.deformed_fft(res,geomdim,defgrad_av,1.0,defgrad)
else:
centroids = damask.core.mesh.deformed_fft(res,geomdim,defgrad_av,1.0,defgrad) centroids = damask.core.mesh.deformed_fft(res,geomdim,defgrad_av,1.0,defgrad)
# ------------------------------------------ process data --------------------------------------- # ------------------------------------------ process data ---------------------------------------
table.data_rewind() table.data_rewind()

55
processing/post/spectral_buildElements.py → processing/post/nodesFromCentroids.py
View File

@ -38,18 +38,21 @@ def index(location,res):
# -------------------------------------------------------------------- # --------------------------------------------------------------------
parser = OptionParser(option_class=extendableOption, usage='%prog options [file[s]]', description = """ parser = OptionParser(option_class=extendableOption, usage='%prog options [file[s]]', description = """
Calculates current coordinates and nodal displacement from IP/FP based deformation gradient. Calculates current nodal coordinates and nodal displacement from IP/FP based data.
""" + string.replace('$Id$','\n','\\n') """ + string.replace('$Id$','\n','\\n')
) )
parser.add_option('-c','--coordinates', dest='coords', type='string',\ parser.add_option('-d','--deformed', dest='deformedCentroids', type='string',\
help='column heading for coordinates [%default]') help='column heading for position of deformed center of element/IP [%default]')
parser.add_option('-d','--defgrad', dest='defgrad', type='string', \ parser.add_option('-u','--undeformed', dest='undeformedCentroids', type='string',\
help='heading of columns containing tensor field values') help='column heading for position of undeformed center of element/IP [%default]')
parser.add_option('-f','--defgrad', dest='defgrad', type='string',\
help='column heading for position of deformation gradient [%default]')
parser.set_defaults(coords = 'ip') parser.set_defaults(deformedCentroids = 'ip_deformed')
parser.set_defaults(defgrad = 'f' ) parser.set_defaults(undeformedCentroids = 'ip')
parser.set_defaults(defgrad = 'f')
(options,filenames) = parser.parse_args() (options,filenames) = parser.parse_args()
@ -75,7 +78,7 @@ for file in files:
# --------------- figure out dimension and resolution # --------------- figure out dimension and resolution
try: try:
locationCol = table.labels.index('%s.x'%options.coords) # columns containing location data locationCol = table.labels.index('%s.x'%options.undeformedCentroids) # columns containing location data
except ValueError: except ValueError:
print 'no coordinate data found...' print 'no coordinate data found...'
continue continue
@ -108,37 +111,49 @@ for file in files:
# --------------- figure out columns to process # --------------- figure out columns to process
key = '%s.x' %options.deformedCentroids
if key not in table.labels:
sys.stderr.write('column %s not found...\n'%key)
else:
columnDeformed = table.labels.index(key)
key = '%s.x' %options.undeformedCentroids
if key not in table.labels:
sys.stderr.write('column %s not found...\n'%key)
else:
columnUndeformed = table.labels.index(key)
key = '1_%s' %options.defgrad key = '1_%s' %options.defgrad
if key not in table.labels: if key not in table.labels:
sys.stderr.write('column %s not found...\n'%key) sys.stderr.write('column %s not found...\n'%key)
else: else:
column = table.labels.index(key) columnDefgrad = table.labels.index(key)
# ------------------------------------------ read value field --------------------------------------- # ------------------------------------------ read value field ---------------------------------------
deformedCentroids = numpy.array([0.0 for i in xrange(N*3)]).reshape(list(res)+[3])
undeformedCentroids = numpy.array([0.0 for i in xrange(N*3)]).reshape(list(res)+[3])
defgrad = numpy.array([0.0 for i in xrange(N*9)]).reshape(list(res)+[3,3]) defgrad = numpy.array([0.0 for i in xrange(N*9)]).reshape(list(res)+[3,3])
table.data_rewind() table.data_rewind()
table.data_read() table.data_read()
inc = table.data[table.labels.index('inc')] inc = int(eval(table.data[table.labels.index('inc')]))
table.data_rewind() table.data_rewind()
idx = 0 idx = 0
while table.data_read(): # read next data line of ASCII table while table.data_read(): # read next data line of ASCII table
(x,y,z) = location(idx,res) # figure out (x,y,z) position from line count (x,y,z) = location(idx,res) # figure out (x,y,z) position from line count
idx += 1 idx += 1
defgrad[x,y,z] = numpy.array(map(float,table.data[column:column+9]),'d').reshape(3,3) deformedCentroids[x,y,z] = numpy.array(map(float,table.data[columnDeformed:columnDeformed+3]),'d')
undeformedCentroids[x,y,z] = numpy.array(map(float,table.data[columnUndeformed:columnUndeformed+3]),'d')
defgrad[x,y,z] = numpy.array(map(float,table.data[columnDefgrad:columnDefgrad+9]),'d').reshape(3,3)
file['input'].close() # close input ASCII table file['input'].close() # close input ASCII table
# ------------------------------------------ process value field ---------------------------- # ------------------------------------------ process value field ----------------------------
defgrad_av = damask.core.math.math_tensorAvg(defgrad)
defgrad_av = damask.core.math.tensorAvg(defgrad) nodesDeformed = damask.core.mesh.mesh_regular_grid(res,geomdim,defgrad_av,deformedCentroids)
centroids = damask.core.mesh.deformed_fft(res,geomdim,defgrad_av,1.0,defgrad) nodesUndeformed = damask.core.mesh.mesh_regular_grid(res,geomdim,numpy.identity(3,'d'),undeformedCentroids)
nodes = damask.core.mesh.mesh_regular_grid(res,geomdim,defgrad_av,centroids)
# ------------------------------------------ process data --------------------------------------- # ------------------------------------------ process data ---------------------------------------
@ -148,7 +163,7 @@ for file in files:
table.labels_append('inc elem node ip grain ') # extend ASCII header with new labels table.labels_append('inc elem node ip grain ') # extend ASCII header with new labels
table.labels_append(['node.%s'%(coord) for coord in 'x','y','z']) # extend ASCII header with new labels table.labels_append(['node.%s'%(coord) for coord in 'x','y','z']) # extend ASCII header with new labels
table.labels_append(['Displacement %s'%(coord) for coord in 'X','Y','Z']) # extend ASCII header with new labels table.labels_append(['Displacement%s'%(coord) for coord in 'X','Y','Z']) # extend ASCII header with new labels
table.head_write() table.head_write()
ielem = 0 ielem = 0
@ -156,7 +171,7 @@ for file in files:
for y in xrange(res[1]+1): for y in xrange(res[1]+1):
for x in xrange(res[0]+1): for x in xrange(res[0]+1):
ielem +=1 ielem +=1
entry = [inc,0,ielem,0,0,'\t'.join([str(a) for a in(nodes[x][y][z])]),'\t'.join([str(a) for a in (nodes[x][y][z] - (x,y,z)*(geomdim/res))])] entry = [inc,0,ielem,0,0,'\t'.join([str(a) for a in(nodesUndeformed[x][y][z])]),'\t'.join([str(a) for a in (nodesUndeformed[x][y][z] - nodesDeformed[x][y][z])])]
table.data_append(entry) table.data_append(entry)
table.data_write() # output processed line table.data_write() # output processed line
table.data_clear() table.data_clear()

194
processing/post/table2ang.py Executable file
View File

@ -0,0 +1,194 @@
#!/usr/bin/env python
import os,re,sys,math,string,damask,numpy
from optparse import OptionParser, Option
# -----------------------------
class extendableOption(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)
def integerFactorization(i):
j = int(math.floor(math.sqrt(float(i))))
while (j>1 and int(i)%j != 0):
j -= 1
return j
def positiveRadians(angle):
angle = math.radians(float(angle))
while angle < 0.0:
angle += 2.0*math.pi
return angle
def getHeader(sizeX,sizeY,step):
return [ \
'# TEM_PIXperUM 1.000000', \
'# x-star 0.509548', \
'# y-star 0.795272', \
'# z-star 0.611799', \
'# WorkingDistance 18.000000', \
'#', \
'# Phase 1', \
'# MaterialName Al', \
'# Formula Fe', \
'# Info', \
'# Symmetry 43', \
'# LatticeConstants 2.870 2.870 2.870 90.000 90.000 90.000', \
'# NumberFamilies 4', \
'# hklFamilies 1 1 0 1 0.000000 1', \
'# hklFamilies 2 0 0 1 0.000000 1', \
'# hklFamilies 2 1 1 1 0.000000 1', \
'# hklFamilies 3 1 0 1 0.000000 1', \
'# Categories 0 0 0 0 0 ', \
'#', \
'# GRID: SquareGrid', \
'# XSTEP: ' + str(step), \
'# YSTEP: ' + str(step), \
'# NCOLS_ODD: ' + str(sizeX), \
'# NCOLS_EVEN: ' + str(sizeX), \
'# NROWS: ' + str(sizeY), \
'#', \
'# OPERATOR: ODFsammpling', \
'#', \
'# SAMPLEID: ', \
'#', \
'# SCANID: ', \
'#', \
]
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(option_class=extendableOption, usage='%prog options [file[s]]', description = """
Builds an ang file out of ASCII table.
""" + string.replace('$Id$','\n','\\n')
)
parser.add_option('--coords', dest='coords', type='string', \
help='label of coords in ASCII table')
parser.set_defaults(norm = 'ip')
(options,filenames) = parser.parse_args()
datainfo = {
'vector': {'len':3,
'label':[]}
}
datainfo['vector']['label'] += ['eulerangles']
# ------------------------------------------ setup file handles ---------------------------------------
files = []
if filenames == []:
files.append({'name':'STDIN', 'input':sys.stdin, 'output':sys.stdout})
else:
for name in filenames:
if os.path.exists(name):
files.append({'name':name, 'input':open(name)})
# ------------------------------------------ loop over input files ---------------------------------------
for file in files:
if file['name'] != 'STDIN': print file['name']
table = damask.ASCIItable(file['input']) # open ASCII_table for reading
table.head_read() # read ASCII header info
# --------------- figure out dimension and resolution
try:
locationCol = table.labels.index('ip.x') # columns containing location data
except ValueError:
print 'no coordinate data found...'
continue
grid = [{},{},{}]
while table.data_read(): # read next data line of ASCII table
for j in xrange(3):
grid[j][str(table.data[locationCol+j])] = True # remember coordinate along x,y,z
resolution = numpy.array([len(grid[0]),\
len(grid[1]),\
len(grid[2]),],'i') # resolution is number of distinct coordinates found
dimension = resolution/numpy.maximum(numpy.ones(3,'d'),resolution-1.0)* \
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[2].keys()))-min(map(float,grid[2].keys())),\
],'d') # dimension from bounding box, corrected for cell-centeredness
if resolution[2] == 1:
dimension[2] = min(dimension[:2]/resolution[:2])
N = resolution.prod()
print '\t%s @ %s'%(dimension,resolution)
# --------------- figure out columns to process
active = {}
column = {}
values = {}
divergence = {}
head = []
for datatype,info in datainfo.items():
for label in info['label']:
key = {True :'1_%s',
False:'%s' }[info['len']>1]%label
if key not in table.labels:
sys.stderr.write('column %s not found...\n'%key)
else:
if datatype not in active: active[datatype] = []
if datatype not in column: column[datatype] = {}
if datatype not in values: values[datatype] = {}
if datatype not in divergence: divergence[datatype] = {}
if label not in divergence[datatype]: divergence[datatype][label] = {}
active[datatype].append(label)
column[datatype][label] = table.labels.index(key) # remember columns of requested data
values[datatype][label] = numpy.array([0.0 for i in xrange(N*datainfo[datatype]['len'])])
# ------------------------------------------ read value field ---------------------------------------
table.data_rewind()
print values['vector']['eulerangles']
print numpy.shape(values['vector']['eulerangles'])
idx = 0
while table.data_read(): # read next data line of ASCII table
for datatype,labels in active.items(): # loop over vector,tensor
for label in labels: # loop over all requested curls
values[datatype][label][idx:idx+3]= numpy.array(map(float,table.data[column[datatype][label]:
column[datatype][label]+datainfo[datatype]['len']]),'d')
idx+=3
for z in xrange(resolution[2]):
fileOut=open(os.path.join(os.path.dirname(name),os.path.splitext(os.path.basename(name))[0]+'_%s.ang'%z),'w')
for line in getHeader(resolution[0],resolution[1],1.0):
fileOut.write(line + '\n')
# write data
for counter in xrange(resolution[0]*resolution[1]):
print z*resolution[0]*resolution[1]*3+counter*3,' - ',z*resolution[0]*resolution[1]*3+counter*3+3
fileOut.write(''.join(['%10.5f'%positiveRadians(angle) for angle in values['vector']['eulerangles'][z*resolution[0]*resolution[1]*3+counter*3:z*resolution[0]*resolution[1]*3+counter*3+3]])+
''.join(['%10.5f'%coord for coord in [counter%resolution[0],counter//resolution[1]]])+
' 100.0 1.0 0 1 1.0\n')
counter += 1
fileOut.close()

3
processing/setup/setup_processing.py
View File

@ -116,8 +116,9 @@ bin_link = { \
'postResults.py', 'postResults.py',
'spectral_iterationCount.py', 'spectral_iterationCount.py',
'spectral_parseLog.py', 'spectral_parseLog.py',
'spectral_buildElements.py', 'nodesFromCentroids.py',
'tagLabel.py', 'tagLabel.py',
'table2ang',
], ],
} }