post processing script to add eigenvalues and eigenvectors to tensorial data in ASCII tables.
This commit is contained in:
Philip Eisenlohr
parent
526e08bd02
commit
255af58434
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#!/usr/bin/env python
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import os,re,sys,math,numpy,string,damask
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from optparse import OptionParser, Option
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# -----------------------------
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class extendableOption(Option):
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# -----------------------------
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# used for definition of new option parser action 'extend', which enables to take multiple option arguments
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# taken from online tutorial http://docs.python.org/library/optparse.html
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ACTIONS = Option.ACTIONS + ("extend",)
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STORE_ACTIONS = Option.STORE_ACTIONS + ("extend",)
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TYPED_ACTIONS = Option.TYPED_ACTIONS + ("extend",)
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ALWAYS_TYPED_ACTIONS = Option.ALWAYS_TYPED_ACTIONS + ("extend",)
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def take_action(self, action, dest, opt, value, values, parser):
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if action == "extend":
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lvalue = value.split(",")
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values.ensure_value(dest, []).extend(lvalue)
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else:
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Option.take_action(self, action, dest, opt, value, values, parser)
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# --------------------------------------------------------------------
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# MAIN
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# --------------------------------------------------------------------
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parser = OptionParser(option_class=extendableOption, usage='%prog options [file[s]]', description = """
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Add column(s) containing eigenvalues and eigenvectors of requested tensor column(s).
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""" + string.replace('$Id$','\n','\\n')
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)
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parser.add_option('-t','--tensor', dest='tensor', action='extend', type='string', \
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help='heading of columns containing tensor field values')
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parser.set_defaults(tensor = [])
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(options,filenames) = parser.parse_args()
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if len(options.tensor) == 0:
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parser.error('no data column specified...')
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datainfo = { # list of requested labels per datatype
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'tensor': {'len':9,
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'label':[]},
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}
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if options.tensor != None: datainfo['tensor']['label'] += options.tensor
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# ------------------------------------------ setup file handles ---------------------------------------
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files = []
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if filenames == []:
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files.append({'name':'STDIN',
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'input':sys.stdin,
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'output':sys.stdout,
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'croak':sys.stderr,
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})
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else:
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for name in filenames:
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if os.path.exists(name):
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files.append({'name':name,
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'input':open(name),
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'output':open(name+'_tmp','w'),
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'croak':sys.stdout,
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})
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# ------------------------------------------ loop over input files ---------------------------------------
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for file in files:
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if file['name'] != 'STDIN': file['croak'].write(file['name']+'\n')
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table = damask.ASCIItable(file['input'],file['output'],False) # make unbuffered ASCII_table
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table.head_read() # read ASCII header info
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table.info_append(string.replace('$Id$','\n','\\n') + \
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'\t' + ' '.join(sys.argv[1:]))
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active = {}
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column = {}
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head = []
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for datatype,info in datainfo.items():
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for label in info['label']:
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key = {True :'1_%s',
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False:'%s' }[info['len']>1]%label
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if key not in table.labels:
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file['croak'].write('column %s not found...\n'%key)
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else:
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if datatype not in active: active[datatype] = []
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if datatype not in column: column[datatype] = {}
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active[datatype].append(label)
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column[datatype][label] = table.labels.index(key) # remember columns of requested data
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table.labels_append(['%i_eigval(%s)'%(i+1,label)
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for i in xrange(3)]) # extend ASCII header with new labels
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table.labels_append(['%i_eigvec(%s)'%(i+1,label)
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for i in xrange(9)]) # extend ASCII header with new labels
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# ------------------------------------------ assemble header ---------------------------------------
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table.head_write()
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# ------------------------------------------ process data ---------------------------------------
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while table.data_read(): # read next data line of ASCII table
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for datatype,labels in active.items(): # loop over vector,tensor
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for label in labels: # loop over all requested norms
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tensor = numpy.array(map(float,table.data[column[datatype][label]:
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column[datatype][label]+datainfo[datatype]['len']])).reshape((datainfo[datatype]['len']//3,3))
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(u,v) = numpy.linalg.eig(tensor)
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table.data_append(list(u))
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table.data_append(list(v.transpose().reshape(datainfo[datatype]['len'])))
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table.data_write() # output processed line
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# ------------------------------------------ output result ---------------------------------------
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table.output_flush() # just in case of buffered ASCII table
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try:
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file['output'].close() # close output ASCII table
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except:
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pass
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try:
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file['croak'].close() # stop croaking
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except:
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pass
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try:
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file['input'].close() # close input ASCII table
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except:
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pass
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if file['name'] != 'STDIN':
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os.rename(file['name']+'_tmp',file['name']) # overwrite old one with tmp new
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@ -101,6 +101,7 @@ bin_link = { \
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'addCalculation.py',
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'addDeterminant.py',
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'addDeviator.py',
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'addSpectralDecomposition.py',
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'addDivergence.py',
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'addCurl.py',
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'addMises.py',
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@ -116,7 +117,6 @@ bin_link = { \
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'filterTable.py',
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'mentat_colorMap.py',
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'postResults.py',
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'spectral_iterationCount.py',
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'spectral_parseLog.py',
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'nodesFromCentroids.py',
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'tagLabel.py',
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