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adopted ASCII_TABLE class

This commit is contained in:
Philip Eisenlohr 2011-12-04 09:57:13 +00:00
parent 42c3074821
commit 9d3f7b8d3d
1 changed files with 36 additions and 80 deletions
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112
processing/post/addStrainTensors.py
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@ -1,16 +1,8 @@
#!/usr/bin/python #!/usr/bin/python
import os,re,sys,math,numpy,string import os,re,sys,math,numpy,string,damask_tools
from optparse import OptionParser, Option from optparse import OptionParser, Option
def operator(how,vector):
return { \
'ln': numpy.log(vector)*1.0,\
'Biot': vector *1.0,\
'Green': vector*vector *0.5,\
}[how]
# ----------------------------- # -----------------------------
class extendableOption(Option): class extendableOption(Option):
# ----------------------------- # -----------------------------
@ -30,10 +22,14 @@ class extendableOption(Option):
Option.take_action(self, action, dest, opt, value, values, parser) Option.take_action(self, action, dest, opt, value, values, parser)
def prefixMultiply(what,len):
return {True: ['%i_%s'%(i+1,what) for i in range(len)], def operator(how,vector):
False:[what]}[len>1] return { \
'ln': numpy.log(vector)*1.0,\
'Biot': vector *1.0,\
'Green': vector*vector *0.5,\
}[how]
# -------------------------------------------------------------------- # --------------------------------------------------------------------
@ -47,8 +43,6 @@ Add column(s) containing given strains based on given stretches of requested def
) )
parser.add_option('-m','--memory', dest='memory', action='store_true', \
help='load complete file into memory [%default]')
parser.add_option('-u','--right', action='store_true', dest='right', \ parser.add_option('-u','--right', action='store_true', dest='right', \
help='calculate strains based on right Cauchy--Green deformation, i.e., C and U') help='calculate strains based on right Cauchy--Green deformation, i.e., C and U')
parser.add_option('-v','--left', action='store_true', dest='left', \ parser.add_option('-v','--left', action='store_true', dest='left', \
@ -62,7 +56,6 @@ parser.add_option('-g','--green', action='store_true', dest='green', \
parser.add_option('-f','--deformation', dest='defgrad', action='extend', type='string', \ parser.add_option('-f','--deformation', dest='defgrad', action='extend', type='string', \
help='heading(s) of columns containing deformation tensor values %default') help='heading(s) of columns containing deformation tensor values %default')
parser.set_defaults(memory = False)
parser.set_defaults(right = False) parser.set_defaults(right = False)
parser.set_defaults(left = False) parser.set_defaults(left = False)
parser.set_defaults(logarithmic = False) parser.set_defaults(logarithmic = False)
@ -104,30 +97,12 @@ else:
# ------------------------------------------ loop over input files --------------------------------------- # ------------------------------------------ loop over input files ---------------------------------------
for file in files: for file in files:
print file['name'] if file['name'] != 'STDIN': print file['name']
# get labels by either read the first row, or - if keyword header is present - the last line of the header table = damask_tools.ASCII_TABLE(file['input'],file['output'],False) # make unbuffered ASCII_table
table.head_read() # read ASCII header info
firstline = file['input'].readline() table.info_append(string.replace('$Id$','\n','\\n') + \
m = re.search('(\d+)\s*head', firstline.lower()) '\t' + ' '.join(sys.argv[1:]))
if m:
headerlines = int(m.group(1))
passOn = [file['input'].readline() for i in range(1,headerlines)]
headers = file['input'].readline().split()
else:
headerlines = 1
passOn = []
headers = firstline.split()
if options.memory:
data = file['input'].readlines()
else:
data = []
for i,l in enumerate(headers):
if l.startswith('1_'):
if re.match('\d+_',l[2:]) or i == len(headers)-1 or not headers[i+1].endswith(l[2:]):
headers[i] = l[2:]
active = {} active = {}
column = {} column = {}
@ -137,50 +112,37 @@ for file in files:
for label in info['label']: for label in info['label']:
key = {True :'1_%s', key = {True :'1_%s',
False:'%s' }[info['len']>1]%label False:'%s' }[info['len']>1]%label
if key not in headers: 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:
if datatype not in active: active[datatype] = [] if datatype not in active: active[datatype] = []
if datatype not in column: column[datatype] = {} if datatype not in column: column[datatype] = {}
active[datatype].append(label) active[datatype].append(label)
column[datatype][label] = headers.index(key) column[datatype][label] = table.labels.index(key)
for theStretch in stretches: for theStretch in stretches:
for theStrain in strains: for theStrain in strains:
head += prefixMultiply('%s(%s)'%(theStrain,theStretch), 9) table.labels_append(['%i_%s(%s)'%(i+1,theStrain,theStretch)
for i in xrange(datainfo['defgrad']['len'])]) # extend ASCII header with new labels
# ------------------------------------------ assemble header --------------------------------------- # ------------------------------------------ assemble header ---------------------------------------
output = '%i\theader'%(headerlines+1) + '\n' + \ table.head_write()
''.join(passOn) + \
string.replace('$Id$','\n','\\n')+ '\t' + \
' '.join(sys.argv[1:]) + '\n' + \
'\t'.join(headers + head) + '\n' # build extended header
if not options.memory: # ------------------------------------------ process data ---------------------------------------
file['output'].write(output)
output = ''
# ------------------------------------------ read file --------------------------------------- while table.data_read(): # read next data line of ASCII table
for line in {True : data, for datatype,labels in active.items(): # loop over vector,tensor
False : file['input']}[options.memory]: for label in labels: # loop over all requested norms
items = line.split()[:len(headers)] F = numpy.array(map(float,table.data[column['defgrad'][active['defgrad'][0]]:
if len(items) < len(headers): column['defgrad'][active['defgrad'][0]]+datainfo['defgrad']['len']]),'d').reshape(3,3)
continue (U,S,Vh) = numpy.linalg.svd(F)
output += '\t'.join(items)
for datatype,labels in active.items():
for label in labels:
defgrad = numpy.array(map(float,items[column[datatype][label]:
column[datatype][label]+datainfo[datatype]['len']]),'d').reshape(3,3)
(U,S,Vh) = numpy.linalg.svd(defgrad)
R = numpy.dot(U,Vh) R = numpy.dot(U,Vh)
stretch['U'] = numpy.dot(numpy.linalg.inv(R),defgrad) stretch['U'] = numpy.dot(numpy.linalg.inv(R),F)
stretch['V'] = numpy.dot(defgrad,numpy.linalg.inv(R)) stretch['V'] = numpy.dot(F,numpy.linalg.inv(R))
for theStretch in stretches: for theStretch in stretches:
for i in range(9): for i in range(9):
if stretch[theStretch][i%3,i//3] < 1e-15: if abs(stretch[theStretch][i%3,i//3]) < 1e-15: # kill nasty noisy data
stretch[theStretch][i%3,i//3] = 0.0 stretch[theStretch][i%3,i//3] = 0.0
(D,V) = numpy.linalg.eig(stretch[theStretch]) # eigen decomposition (of symmetric matrix) (D,V) = numpy.linalg.eig(stretch[theStretch]) # eigen decomposition (of symmetric matrix)
for i,eigval in enumerate(D): for i,eigval in enumerate(D):
@ -194,22 +156,16 @@ for file in files:
d = operator(theStrain,D) # operate on eigenvalues of U or V d = operator(theStrain,D) # operate on eigenvalues of U or V
I = operator(theStrain,numpy.ones(3)) # operate on eigenvalues of I (i.e. [1,1,1]) I = operator(theStrain,numpy.ones(3)) # operate on eigenvalues of I (i.e. [1,1,1])
eps = (numpy.dot(V,numpy.dot(numpy.diag(d),V.T)).real-numpy.diag(I)).reshape(9) # build tensor back from eigenvalue/vector basis eps = (numpy.dot(V,numpy.dot(numpy.diag(d),V.T)).real-numpy.diag(I)).reshape(9) # build tensor back from eigenvalue/vector basis
output += '\t'+'\t'.join(map(str,eps))
table.data_append(list(eps))
output += '\n' table.data_write() # output processed line
if not options.memory:
file['output'].write(output)
output = ''
file['input'].close()
# ------------------------------------------ output result --------------------------------------- # ------------------------------------------ output result ---------------------------------------
if options.memory: table.output_flush() # just in case of buffered ASCII table
file['output'].write(output)
file['input'].close() # close input ASCII table
if file['name'] != 'STDIN': if file['name'] != 'STDIN':
file['output'].close file['output'].close # close output ASCII table
os.rename(file['name']+'_tmp',file['name']) os.rename(file['name']+'_tmp',file['name']) # overwrite old one with tmp new