updated first 9 post processing scripts to latest ASCII table handling style
This commit is contained in:
Martin Diehl
parent
c8cd775747
commit
e8d2e787bc
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@ -87,28 +87,29 @@ for file in files:
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if label not in brokenFormula:
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evaluator[label] = "'" + formula + "'%(" + ','.join(interpolator) + ")"
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# ------------------------------------------ calculate one result to get length of labels ---------
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table.data_read()
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labelLen = {}
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for label in options.labels:
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labelLen[label] = np.size(eval(eval(evaluator[label])))
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# ------------------------------------------ assemble header ---------------------------------------
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for label,formula in zip(options.labels,options.formulas):
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if labelLen[label] == 0:
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brokenFormula[label] = True
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if label not in brokenFormula:
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if labelLen[label] == 1:
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table.labels_append(label)
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else:
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table.labels_append(['%i_%s'%(i+1,label) for i in xrange(labelLen[label])])
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table.head_write()
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# ------------------------------------------ process data ---------------------------------------
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# ------------------------------------------ process data ------------------------------------------
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firstLine=True
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outputAlive = True
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table.data_rewind()
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while outputAlive and table.data_read(): # read next data line of ASCII table
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specials['_row_'] += 1 # count row
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# ------------------------------------------ calculate one result to get length of labels ---------
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if firstLine:
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labelLen = {}
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for label in options.labels:
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labelLen[label] = np.size(eval(eval(evaluator[label])))
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# ------------------------------------------ assemble header ---------------------------------------
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for label,formula in zip(options.labels,options.formulas):
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if labelLen[label] == 0:
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brokenFormula[label] = True
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if label not in brokenFormula:
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if labelLen[label] == 1:
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table.labels_append(label)
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else:
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table.labels_append(['%i_%s'%(i+1,label) for i in xrange(labelLen[label])])
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table.head_write()
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firstLine = False
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for label in options.labels: table.data_append(unravel(eval(eval(evaluator[label]))))
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outputAlive = table.data_write() # output processed line
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@ -30,19 +30,13 @@ parser.set_defaults(stress = 'p')
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(options,filenames) = parser.parse_args()
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if options.defgrad == None or options.stress == None:
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parser.error('missing data column...')
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datainfo = { # list of requested labels per datatype
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'defgrad': {'mandatory': True,
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'len':9,
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'defgrad': {'len':9,
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'label':[]},
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'stress': {'mandatory': True,
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'len':9,
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'stress': {'len':9,
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'label':[]},
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}
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datainfo['defgrad']['label'].append(options.defgrad)
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datainfo['stress']['label'].append(options.stress)
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@ -74,21 +68,20 @@ for file in files:
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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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missingColumns |= info['mandatory'] # break if label is mandatory
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missingColumns = True # break if label not found
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else:
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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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if missingColumns:
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continue
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# ------------------------------------------ assemble header ---------------------------------------
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table.labels_append(['%i_Cauchy'%(i+1)
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for i in xrange(datainfo['stress']['len'])]) # extend ASCII header with new labels
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# ------------------------------------------ assemble header ------------------------------------
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table.labels_append(['%i_Cauchy'%(i+1) for i in xrange(datainfo['stress']['len'])]) # extend ASCII header with new labels
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table.head_write()
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# ------------------------------------------ process data ---------------------------------------
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# ------------------------------------------ process data ----------------------------------------
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outputAlive = True
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table.data_rewind()
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while outputAlive and table.data_read(): # read next data line of ASCII table
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F = np.array(map(float,table.data[column['defgrad'][active['defgrad'][0]]:
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column['defgrad'][active['defgrad'][0]]+datainfo['defgrad']['len']]),'d').reshape(3,3)
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@ -3,7 +3,6 @@
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import os,re,sys,math,string
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import numpy as np
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from collections import defaultdict
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from optparse import OptionParser
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import damask
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@ -45,48 +44,25 @@ datainfo['defgrad']['label'].append(options.defgrad)
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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', 'input':sys.stdin, 'output':sys.stdout, 'croak':sys.stderr})
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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, 'input':open(name), 'output':open(name+'_tmp','w'), 'croak':sys.stderr})
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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, 'input':open(name), 'output':open(name+'_tmp','w'), 'croak':sys.stderr})
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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('\033[1m'+scriptName+'\033[0m: '+file['name']+'\n')
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else: file['croak'].write('\033[1m'+scriptName+'\033[0m\n')
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file['croak'].write('\033[1m'+scriptName+'\033[0m: '+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(scriptID,'\n','\\n') + '\t' + ' '.join(sys.argv[1:]))
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# --------------- figure out dimension and resolution --------------------------------------------------
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# --------------- figure out dimension and resolution ----------------------------------------------
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try:
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locationCol = table.labels.index('%s.x'%options.coords) # columns containing location data
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except ValueError:
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file['croak'].write('no coordinate data found...\n'%key)
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continue
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active = defaultdict(list)
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column = defaultdict(dict)
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missingColumns = False
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for datatype,info in datainfo.items():
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for label in info['label']:
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key = '1_%s'%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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missingColumns = True
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else:
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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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column = table.labels.index(key)
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if missingColumns:
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continue
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# --------------- figure out dimension and resolution ---------------------------------------------
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grid = [{},{},{}]
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while table.data_read(): # read next data line of ASCII table
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for j in xrange(3):
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@ -103,6 +79,21 @@ for file in files:
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geomdim[2] = min(geomdim[:2]/res[:2])
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N = res.prod()
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# --------------- figure out columns to process ---------------------------------------------------
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missingColumns = False
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for datatype,info in datainfo.items():
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for label in info['label']:
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key = '1_%s'%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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missingColumns = True
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else:
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column = table.labels.index(key) # remember columns of requested data
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if missingColumns:
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continue
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# ------------------------------------------ assemble header ---------------------------------------
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if not options.noShape: table.labels_append(['shapeMismatch(%s)' %options.defgrad])
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if not options.noVolume: table.labels_append(['volMismatch(%s)'%options.defgrad])
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@ -112,7 +103,8 @@ for file in files:
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table.data_rewind()
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F = np.array([0.0 for i in xrange(N*9)]).reshape([3,3]+list(res))
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idx = 0
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(x,y,z) = damask.gridLocation(idx,res) # figure out (x,y,z) position from line count
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while table.data_read():
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(x,y,z) = damask.util.gridLocation(idx,res) # figure out (x,y,z) position from line count
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idx += 1
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F[0:3,0:3,x,y,z] = np.array(map(float,table.data[column:column+9]),'d').reshape(3,3)
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@ -125,20 +117,18 @@ for file in files:
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# ------------------------------------------ process data ---------------------------------------
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table.data_rewind()
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outputAlive = True
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idx = 0
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while outputAlive and table.data_read(): # read next data line of ASCII table
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(x,y,z) = damask.gridLocation(idx,res ) # figure out (x,y,z) position from line count
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outputAlive = True
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while outputAlive and table.data_read(): # read next data line of ASCII table
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(x,y,z) = damask.util.gridLocation(idx,res) # figure out (x,y,z) position from line count
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idx += 1
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if not options.noShape: table.data_append( shapeMismatch[x,y,z])
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if not options.noVolume: table.data_append(volumeMismatch[x,y,z])
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outputAlive = table.data_write() # output processed line
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outputAlive = table.data_write() # output processed line
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# ------------------------------------------ output result ---------------------------------------
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outputAlive and table.output_flush() # just in case of buffered ASCII table
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file['input'].close() # close input ASCII table (works for stdin)
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file['output'].close() # close output ASCII table (works for stdout)
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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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os.rename(file['name']+'_tmp',file['name']) # overwrite old one with tmp new
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@ -89,14 +89,13 @@ for file in files:
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column = defaultdict(dict)
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values = defaultdict(dict)
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curl = defaultdict(dict)
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missingColumns = False
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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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sys.stderr.write('column %s not found...\n'%key)
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file['croak'].write('column %s not found...\n'%key)
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else:
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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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@ -104,15 +103,12 @@ for file in files:
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reshape(list(resolution)+[datainfo[datatype]['len']//3,3])
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curl[datatype][label] = np.array([0.0 for i in xrange(N*datainfo[datatype]['len'])]).\
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reshape(list(resolution)+[datainfo[datatype]['len']//3,3])
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if missingColumns:
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continue
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# ------------------------------------------ assemble header ---------------------------------------
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for datatype,info in datainfo.items():
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for label in info['label']:
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table.labels_append(['%i_curlFFT(%s)'%(i+1,label)
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for i in xrange(datainfo[datatype]['len'])]) # extend ASCII header with new labels
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for datatype,labels in active.items(): # loop over vector,tensor
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for label in labels:
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table.labels_append(['%i_curlFFT(%s)'%(i+1,label)
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for i in xrange(datainfo[datatype]['len'])]) # extend ASCII header with new labels
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table.head_write()
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# ------------------------------------------ read value field --------------------------------------
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@ -1,166 +1,130 @@
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#!/usr/bin/env python
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# -*- coding: UTF-8 no BOM -*-
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import os,re,sys,math,string,numpy,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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def location(idx,res):
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return ( idx % res[0], \
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( idx // res[0]) % res[1], \
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( idx // res[0] // res[1]) % res[2] )
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def index(location,res):
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return ( location[0] % res[0] + \
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( location[1] % res[1]) * res[0] + \
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( location[2] % res[2]) * res[1] * res[0] )
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import os,re,sys,math,string
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import numpy as np
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from collections import defaultdict
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from optparse import OptionParser
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import damask
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scriptID = '$Id$'
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scriptName = scriptID.split()[1]
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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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parser = OptionParser(option_class=damask.extendableOption, usage='%prog options file[s]', description = """
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Add column(s) containing deformed configuration of requested column(s).
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Operates on periodic ordered three-dimensional data sets.
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""" + string.replace('$Id$','\n','\\n')
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""", version = string.replace(scriptID,'\n','\\n')
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)
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parser.add_option('-c','--coordinates', dest='coords', type='string',\
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parser.add_option('-c','--coordinates', dest='coords', type='string', metavar='string', \
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help='column heading for coordinates [%default]')
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parser.add_option('-d','--defgrad', dest='defgrad', type='string', \
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parser.add_option('-d','--defgrad', dest='defgrad', type='string', metavar='string', \
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help='heading of columns containing tensor field values')
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parser.add_option('-l', '--linear', dest='linearreconstruction', action='store_true',\
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help='use linear reconstruction of geometry [%default]')
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parser.add_option('-l', '--linear', dest='linearreconstruction', action='store_true',\
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help='use linear reconstruction of geometry [%default]')
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parser.set_defaults(coords = 'ip')
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parser.set_defaults(defgrad = 'f' )
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parser.set_defaults(linearreconstruction = False)
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(options,filenames) = parser.parse_args()
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# ------------------------------------------ setup file handles ---------------------------------------
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datainfo = { # list of requested labels per datatype
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'defgrad': {'len':9,
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'label':[]},
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}
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datainfo['defgrad']['label'].append(options.defgrad)
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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', 'input':sys.stdin, 'output':sys.stdout})
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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, 'input':open(name), 'output':open(name+'_tmp','w')})
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# ------------------------------------------ loop over input files ---------------------------------------
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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, 'input':open(name), 'output':open(name+'_tmp','w'), 'croak':sys.stderr})
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#--- loop over input files ------------------------------------------------------------------------
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for file in files:
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if file['name'] != 'STDIN': print file['name'],
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file['croak'].write('\033[1m'+scriptName+'\033[0m: '+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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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(scriptID,'\n','\\n') + '\t' + ' '.join(sys.argv[1:]))
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# --------------- figure out dimension and resolution
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# --------------- figure out dimension and resolution ----------------------------------------------
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try:
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locationCol = table.labels.index('%s.x'%options.coords) # columns containing location data
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locationCol = table.labels.index('%s.x'%options.coords) # columns containing location data
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except ValueError:
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print 'no coordinate data found...'
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file['croak'].write('no coordinate data found...\n'%key)
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continue
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grid = [{},{},{}]
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while table.data_read(): # read next data line of ASCII table
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if str(table.data[locationCol+1]) in grid[1] and len(grid[1])>1: # geomdim[1] and res[1] already figured out, skip layers
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table.data_skipLines(len(grid[1])*len(grid[0])-1)
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else:
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if str(table.data[locationCol]) in grid[0]: # geomdim[0] and res[0] already figured out, skip lines
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table.data_skipLines(len(grid[0])-1)
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while table.data_read(): # read next data line of ASCII table
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for j in xrange(3):
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grid[j][str(table.data[locationCol+j])] = True # remember coordinate along x,y,z
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res = numpy.array([len(grid[0]),\
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len(grid[1]),\
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len(grid[2]),],'i') # resolution is number of distinct coordinates found
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geomdim = res/numpy.maximum(numpy.ones(3,'d'),res-1.0)* \
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numpy.array([max(map(float,grid[0].keys()))-min(map(float,grid[0].keys())),\
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max(map(float,grid[1].keys()))-min(map(float,grid[1].keys())),\
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max(map(float,grid[2].keys()))-min(map(float,grid[2].keys())),\
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],'d') # dimension from bounding box, corrected for cell-centeredness
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grid[j][str(table.data[locationCol+j])] = True # remember coordinate along x,y,z
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res = np.array([len(grid[0]),\
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len(grid[1]),\
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len(grid[2]),],'i') # resolution is number of distinct coordinates found
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geomdim = res/np.maximum(np.ones(3,'d'),res-1.0)* \
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np.array([max(map(float,grid[0].keys()))-min(map(float,grid[0].keys())),\
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max(map(float,grid[1].keys()))-min(map(float,grid[1].keys())),\
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max(map(float,grid[2].keys()))-min(map(float,grid[2].keys())),\
|
||||
],'d') # dimension from bounding box, corrected for cell-centeredness
|
||||
if res[2] == 1:
|
||||
geomdim[2] = min(geomdim[:2]/res[:2])
|
||||
|
||||
geomdim[2] = min(geomdim[:2]/res[:2])
|
||||
N = res.prod()
|
||||
print '\t%s @ %s'%(geomdim,res)
|
||||
|
||||
# --------------- figure out columns to process ---------------------------------------------------
|
||||
missingColumns = False
|
||||
|
||||
# --------------- figure out columns to process
|
||||
for datatype,info in datainfo.items():
|
||||
for label in info['label']:
|
||||
key = '1_%s'%label
|
||||
if key not in table.labels:
|
||||
file['croak'].write('column %s not found...\n'%key)
|
||||
missingColumns = True
|
||||
else:
|
||||
column = table.labels.index(key) # remember columns of requested data
|
||||
|
||||
key = '1_%s' %options.defgrad
|
||||
if key not in table.labels:
|
||||
sys.stderr.write('column %s not found...\n'%key)
|
||||
else:
|
||||
F = numpy.array([0.0 for i in xrange(N*9)]).reshape([3,3]+list(res))
|
||||
table.labels_append(['%s_coordsMod'%(coord+1) for coord in xrange(3)]) # extend ASCII header with new labels
|
||||
|
||||
column = table.labels.index(key)
|
||||
if missingColumns:
|
||||
continue
|
||||
|
||||
# ------------------------------------------ assemble header ---------------------------------------
|
||||
|
||||
table.labels_append(['%s_coords'%(coord+1) for coord in xrange(3)]) # extend ASCII header with new labels
|
||||
table.head_write()
|
||||
|
||||
# ------------------------------------------ read value field ---------------------------------------
|
||||
|
||||
# ------------------------------------------ read deformation gradient field -----------------------
|
||||
table.data_rewind()
|
||||
|
||||
F = np.array([0.0 for i in xrange(N*9)]).reshape([3,3]+list(res))
|
||||
idx = 0
|
||||
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
|
||||
while table.data_read():
|
||||
(x,y,z) = damask.util.gridLocation(idx,res) # figure out (x,y,z) position from line count
|
||||
idx += 1
|
||||
F[:,:,x,y,z] = numpy.array(map(float,table.data[column:column+9]),'d').reshape(3,3)
|
||||
F[0:3,0:3,x,y,z] = np.array(map(float,table.data[column:column+9]),'d').reshape(3,3)
|
||||
|
||||
# ------------------------------------------ process value field ----------------------------
|
||||
# ------------------------------------------ calculate coordinates ---------------------------------
|
||||
Favg = damask.core.math.tensorAvg(F)
|
||||
if options.linearreconstruction:
|
||||
centroids = damask.core.mesh.deformedCoordsLin(geomdim,F,Favg)
|
||||
else:
|
||||
centroids = damask.core.mesh.deformedCoordsFFT(geomdim,F,Favg)
|
||||
|
||||
# ------------------------------------------ process data ---------------------------------------
|
||||
|
||||
# ------------------------------------------ process data ------------------------------------------
|
||||
table.data_rewind()
|
||||
idx = 0
|
||||
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
|
||||
outputAlive = True
|
||||
while outputAlive and table.data_read(): # read next data line of ASCII table
|
||||
(x,y,z) = damask.util.gridLocation(idx,res) # figure out (x,y,z) position from line count
|
||||
idx += 1
|
||||
table.data_append(list(centroids[:,x,y,z]))
|
||||
|
||||
table.data_write() # output processed line
|
||||
|
||||
outputAlive = table.data_write() # output processed line
|
||||
|
||||
# ------------------------------------------ output result ---------------------------------------
|
||||
outputAlive and table.output_flush() # just in case of buffered ASCII table
|
||||
|
||||
table.output_flush() # just in case of buffered ASCII table
|
||||
|
||||
file['input'].close() # close input ASCII table
|
||||
if file['name'] != 'STDIN':
|
||||
file['output'].close # close output ASCII table
|
||||
os.rename(file['name']+'_tmp',file['name']) # overwrite old one with tmp new
|
||||
file['input'].close() # close input ASCII table (works for stdin)
|
||||
file['output'].close() # close output ASCII table (works for stdout)
|
||||
os.rename(file['name']+'_tmp',file['name']) # overwrite old one with tmp new
|
||||
|
|
|
|||
|
|
@ -1,53 +1,34 @@
|
|||
#!/usr/bin/env python
|
||||
# -*- coding: UTF-8 no BOM -*-
|
||||
|
||||
import os,re,sys,math,string,damask
|
||||
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)
|
||||
|
||||
import os,re,sys,math,string
|
||||
from collections import defaultdict
|
||||
from optparse import OptionParser
|
||||
import damask
|
||||
|
||||
scriptID = '$Id$'
|
||||
scriptName = scriptID.split()[1]
|
||||
|
||||
def determinant(m):
|
||||
|
||||
return +m[0]*m[4]*m[8] \
|
||||
+m[1]*m[5]*m[6] \
|
||||
+m[2]*m[3]*m[7] \
|
||||
-m[2]*m[4]*m[6] \
|
||||
-m[1]*m[3]*m[8] \
|
||||
-m[0]*m[5]*m[7] \
|
||||
|
||||
-m[0]*m[5]*m[7]
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
# MAIN
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
parser = OptionParser(option_class=extendableOption, usage='%prog options [file[s]]', description = """
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
|
||||
Add column(s) containing determinant of requested tensor column(s).
|
||||
|
||||
""" + string.replace('$Id$','\n','\\n')
|
||||
""", version=string.replace(scriptID,'\n','\\n')
|
||||
)
|
||||
|
||||
|
||||
parser.add_option('-t','--tensor', dest='tensor', action='extend', type='string', \
|
||||
parser.add_option('-t','--tensor', dest='tensor', action='extend', type='string', metavar='<string LIST>', \
|
||||
help='heading of columns containing tensor field values')
|
||||
|
||||
parser.set_defaults(tensor = [])
|
||||
|
||||
(options,filenames) = parser.parse_args()
|
||||
|
|
@ -55,73 +36,64 @@ parser.set_defaults(tensor = [])
|
|||
if len(options.tensor) == 0:
|
||||
parser.error('no data column specified...')
|
||||
|
||||
datainfo = { # list of requested labels per datatype
|
||||
datainfo = { # list of requested labels per datatype
|
||||
'tensor': {'len':9,
|
||||
'label':[]},
|
||||
}
|
||||
|
||||
datainfo['tensor']['label'] += options.tensor
|
||||
|
||||
if options.tensor != None: datainfo['tensor']['label'] += options.tensor
|
||||
|
||||
|
||||
|
||||
# ------------------------------------------ setup file handles ---------------------------------------
|
||||
|
||||
# ------------------------------------------ setup file handles -----------------------------------
|
||||
files = []
|
||||
if filenames == []:
|
||||
files.append({'name':'STDIN', 'input':sys.stdin, 'output':sys.stdout})
|
||||
files.append({'name':'STDIN', 'input':sys.stdin, 'output':sys.stdout, 'croak':sys.stderr})
|
||||
else:
|
||||
for name in filenames:
|
||||
if os.path.exists(name):
|
||||
files.append({'name':name, 'input':open(name), 'output':open(name+'_tmp','w')})
|
||||
|
||||
# ------------------------------------------ loop over input files ---------------------------------------
|
||||
files.append({'name':name, 'input':open(name), 'output':open(name+'_tmp','w'), 'croak':sys.stderr})
|
||||
|
||||
#--- loop over input files ------------------------------------------------------------------------
|
||||
for file in files:
|
||||
if file['name'] != 'STDIN': print file['name']
|
||||
if file['name'] != 'STDIN': file['croak'].write('\033[1m'+scriptName+'\033[0m: '+file['name']+'\n')
|
||||
else: file['croak'].write('\033[1m'+scriptName+'\033[0m\n')
|
||||
|
||||
table = damask.ASCIItable(file['input'],file['output'],False) # make unbuffered ASCII_table
|
||||
table.head_read() # read ASCII header info
|
||||
table.info_append(string.replace('$Id$','\n','\\n') + \
|
||||
'\t' + ' '.join(sys.argv[1:]))
|
||||
table = damask.ASCIItable(file['input'],file['output'],False) # make unbuffered ASCII_table
|
||||
table.head_read() # read ASCII header info
|
||||
table.info_append(string.replace(scriptID,'\n','\\n') + '\t' + ' '.join(sys.argv[1:]))
|
||||
|
||||
active = {}
|
||||
column = {}
|
||||
head = []
|
||||
active = defaultdict(list)
|
||||
column = defaultdict(dict)
|
||||
|
||||
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)
|
||||
file['croak'].write('column %s not found...\n'%key)
|
||||
else:
|
||||
if datatype not in active: active[datatype] = []
|
||||
if datatype not in column: column[datatype] = {}
|
||||
active[datatype].append(label)
|
||||
column[datatype][label] = table.labels.index(key) # remember columns of requested data
|
||||
table.labels_append('det(%s)'%label) # extend ASCII header with new labels
|
||||
|
||||
# ------------------------------------------ assemble header ---------------------------------------
|
||||
column[datatype][label] = table.labels.index(key) # remember columns of requested data
|
||||
|
||||
# ------------------------------------------ assemble header ---------------------------------------
|
||||
for datatype,labels in active.items(): # loop over vector,tensor
|
||||
for label in labels: # loop over all requested determinants
|
||||
table.labels_append('det(%s)'%label) # extend ASCII header with new labels
|
||||
table.head_write()
|
||||
|
||||
# ------------------------------------------ process data ---------------------------------------
|
||||
|
||||
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 norms
|
||||
outputAlive = True
|
||||
while outputAlive and 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 determinantes
|
||||
table.data_append(determinant(map(float,table.data[column[datatype][label]:
|
||||
column[datatype][label]+datainfo[datatype]['len']])))
|
||||
|
||||
table.data_write() # output processed line
|
||||
outputAlive = table.data_write() # output processed line
|
||||
|
||||
# ------------------------------------------ output result ---------------------------------------
|
||||
outputAlive and table.output_flush() # just in case of buffered ASCII table
|
||||
|
||||
table.output_flush() # just in case of buffered ASCII table
|
||||
|
||||
file['input'].close() # close input ASCII table
|
||||
file['input'].close() # close input ASCII table (works for stdin)
|
||||
file['output'].close() # close output ASCII table (works for stdout)
|
||||
if file['name'] != 'STDIN':
|
||||
file['output'].close # close output ASCII table
|
||||
os.rename(file['name']+'_tmp',file['name']) # overwrite old one with tmp new
|
||||
os.rename(file['name']+'_tmp',file['name']) # overwrite old one with tmp new
|
||||
|
|
|
|||
|
|
@ -1,29 +1,15 @@
|
|||
#!/usr/bin/env python
|
||||
# -*- coding: UTF-8 no BOM -*-
|
||||
|
||||
import os,re,sys,math,string,damask
|
||||
from optparse import OptionParser, Option
|
||||
import os,re,sys,math,string
|
||||
from collections import defaultdict
|
||||
from optparse import OptionParser
|
||||
import damask
|
||||
|
||||
scriptID = '$Id$'
|
||||
scriptName = scriptID.split()[1]
|
||||
|
||||
oneThird = 1.0/3.0
|
||||
# -----------------------------
|
||||
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 deviator(m):
|
||||
sph = oneThird*(m[0]+m[4]+m[8])
|
||||
|
|
@ -32,19 +18,17 @@ def deviator(m):
|
|||
m[8] = m[8] - sph
|
||||
return m
|
||||
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
# MAIN
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
parser = OptionParser(option_class=extendableOption, usage='%prog options [file[s]]', description = """
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
|
||||
Add column(s) containing deviator of requested tensor column(s).
|
||||
|
||||
""" + string.replace('$Id$','\n','\\n')
|
||||
""", version = string.replace(scriptID,'\n','\\n')
|
||||
)
|
||||
|
||||
|
||||
parser.add_option('-t','--tensor', dest='tensor', action='extend', type='string', \
|
||||
parser.add_option('-t','--tensor', dest='tensor', action='extend', type='string', metavar='<string LIST>', \
|
||||
help='heading of columns containing tensor field values')
|
||||
parser.add_option('-s','--spherical', dest='hydrostatic', action='store_true',\
|
||||
help='also add sperical part of tensor (hydrostatic component, pressure)')
|
||||
|
|
@ -56,76 +40,67 @@ parser.set_defaults(tensor = [])
|
|||
if len(options.tensor) == 0:
|
||||
parser.error('no data column specified...')
|
||||
|
||||
datainfo = { # list of requested labels per datatype
|
||||
datainfo = { # list of requested labels per datatype
|
||||
'tensor': {'len':9,
|
||||
'label':[]},
|
||||
}
|
||||
|
||||
datainfo['tensor']['label'] += options.tensor
|
||||
|
||||
if options.tensor != None: datainfo['tensor']['label'] += options.tensor
|
||||
|
||||
|
||||
|
||||
# ------------------------------------------ setup file handles ---------------------------------------
|
||||
|
||||
# ------------------------------------------ setup file handles -----------------------------------
|
||||
files = []
|
||||
if filenames == []:
|
||||
files.append({'name':'STDIN', 'input':sys.stdin, 'output':sys.stdout})
|
||||
files.append({'name':'STDIN', 'input':sys.stdin, 'output':sys.stdout, 'croak':sys.stderr})
|
||||
else:
|
||||
for name in filenames:
|
||||
if os.path.exists(name):
|
||||
files.append({'name':name, 'input':open(name), 'output':open(name+'_tmp','w')})
|
||||
files.append({'name':name, 'input':open(name), 'output':open(name+'_tmp','w'), 'croak':sys.stderr})
|
||||
|
||||
# ------------------------------------------ loop over input files ---------------------------------------
|
||||
|
||||
for file in files:
|
||||
if file['name'] != 'STDIN': print file['name']
|
||||
if file['name'] != 'STDIN': file['croak'].write('\033[1m'+scriptName+'\033[0m: '+file['name']+'\n')
|
||||
else: file['croak'].write('\033[1m'+scriptName+'\033[0m\n')
|
||||
|
||||
table = damask.ASCIItable(file['input'],file['output'],False) # make unbuffered ASCII_table
|
||||
table.head_read() # read ASCII header info
|
||||
table.info_append(string.replace('$Id$','\n','\\n') + \
|
||||
'\t' + ' '.join(sys.argv[1:]))
|
||||
table = damask.ASCIItable(file['input'],file['output'],False) # make unbuffered ASCII_table
|
||||
table.head_read() # read ASCII header info
|
||||
table.info_append(string.replace(scriptID,'\n','\\n') + '\t' + ' '.join(sys.argv[1:]))
|
||||
|
||||
active = {}
|
||||
column = {}
|
||||
head = []
|
||||
active = defaultdict(list)
|
||||
column = defaultdict(dict)
|
||||
|
||||
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)
|
||||
file['croak'].write('column %s not found...\n'%key)
|
||||
else:
|
||||
if datatype not in active: active[datatype] = []
|
||||
if datatype not in column: column[datatype] = {}
|
||||
active[datatype].append(label)
|
||||
column[datatype][label] = table.labels.index(key) # remember columns of requested data
|
||||
table.labels_append(['%i_dev(%s)'%(i+1,label) for i in xrange(9)]) # extend ASCII header with new labels
|
||||
if(options.hydrostatic): table.labels_append('sph(%s)'%label)
|
||||
|
||||
# ------------------------------------------ assemble header ---------------------------------------
|
||||
column[datatype][label] = table.labels.index(key) # remember columns of requested data
|
||||
|
||||
# ------------------------------------------ assemble header ---------------------------------------
|
||||
for datatype,labels in active.items(): # loop over vector,tensor
|
||||
for label in labels: # loop over all requested determinants
|
||||
table.labels_append(['%i_dev(%s)'%(i+1,label) for i in xrange(9)]) # extend ASCII header with new labels
|
||||
if(options.hydrostatic): table.labels_append('sph(%s)'%label)
|
||||
table.head_write()
|
||||
|
||||
# ------------------------------------------ process data ---------------------------------------
|
||||
|
||||
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 deviators
|
||||
outputAlive = True
|
||||
while outputAlive and 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 deviators
|
||||
myTensor = map(float,table.data[column[datatype][label]:
|
||||
column[datatype][label]+datainfo[datatype]['len']])
|
||||
table.data_append(deviator(myTensor))
|
||||
if(options.hydrostatic): table.data_append(oneThird*(myTensor[0]+myTensor[4]+myTensor[8]))
|
||||
|
||||
table.data_write() # output processed line
|
||||
outputAlive = table.data_write() # output processed line
|
||||
|
||||
# ------------------------------------------ output result ---------------------------------------
|
||||
outputAlive and table.output_flush() # just in case of buffered ASCII table
|
||||
|
||||
table.output_flush() # just in case of buffered ASCII table
|
||||
|
||||
file['input'].close() # close input ASCII table
|
||||
file['input'].close() # close input ASCII table (works for stdin)
|
||||
file['output'].close() # close output ASCII table (works for stdout)
|
||||
if file['name'] != 'STDIN':
|
||||
file['output'].close # close output ASCII table
|
||||
os.rename(file['name']+'_tmp',file['name']) # overwrite old one with tmp new
|
||||
os.rename(file['name']+'_tmp',file['name']) # overwrite old one with tmp new
|
||||
|
|
|
|||
|
|
@ -103,14 +103,13 @@ for file in files:
|
|||
column = defaultdict(dict)
|
||||
values = defaultdict(dict)
|
||||
divergence = defaultdict(dict)
|
||||
missingColumns = False
|
||||
|
||||
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)
|
||||
file['croak'].write('column %s not found...\n'%key)
|
||||
else:
|
||||
active[datatype].append(label)
|
||||
column[datatype][label] = table.labels.index(key) # remember columns of requested data
|
||||
|
|
@ -120,13 +119,10 @@ for file in files:
|
|||
for accuracy in options.accuracy:
|
||||
divergence[datatype][label][accuracy] = np.array([0.0 for i in xrange(N*datainfo[datatype]['len']//3)]).\
|
||||
reshape(list(resolution)+[datainfo[datatype]['len']//3])
|
||||
|
||||
if missingColumns:
|
||||
continue
|
||||
|
||||
# ------------------------------------------ assemble header ---------------------------------------
|
||||
for datatype,info in datainfo.items():
|
||||
for label in info['label']:
|
||||
for datatype,labels in active.items(): # loop over vector,tensor
|
||||
for label in labels:
|
||||
for accuracy in options.accuracy:
|
||||
if datatype == 'vector': # extend ASCII header with new labels
|
||||
table.labels_append(['div%s(%s)'%(accuracy,label)])
|
||||
|
|
|
|||
|
|
@ -1,31 +1,17 @@
|
|||
#!/usr/bin/env python
|
||||
# -*- coding: UTF-8 no BOM -*-
|
||||
|
||||
import os,re,sys,math,numpy,string,damask
|
||||
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)
|
||||
|
||||
import os,re,sys,math,string
|
||||
import numpy as np
|
||||
from collections import defaultdict
|
||||
from optparse import OptionParser
|
||||
import damask
|
||||
|
||||
scriptID = '$Id$'
|
||||
scriptName = scriptID.split()[1]
|
||||
|
||||
def normalize(vec):
|
||||
return vec/numpy.sqrt(numpy.inner(vec,vec))
|
||||
return vec/np.sqrt(np.inner(vec,vec))
|
||||
|
||||
def E_hkl(stiffness,vec): # stiffness = (c11,c12,c44)
|
||||
v = normalize(vec)
|
||||
|
|
@ -36,7 +22,7 @@ def E_hkl(stiffness,vec): # stiffness = (c11,c12,c44)
|
|||
invE = S11-(S11-S12-0.5*S44)* (1.0 - \
|
||||
(v[0]**4+v[1]**4+v[2]**4) \
|
||||
/#------------------------------------
|
||||
numpy.inner(v,v)**2 \
|
||||
np.inner(v,v)**2 \
|
||||
)
|
||||
|
||||
return 1.0/invE
|
||||
|
|
@ -45,20 +31,18 @@ def E_hkl(stiffness,vec): # stiffness = (c11,c12,c44)
|
|||
# MAIN
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
parser = OptionParser(option_class=extendableOption, usage='%prog options [file[s]]', description = """
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
|
||||
Add column(s) containing directional stiffness
|
||||
based on given cubic stiffness values C11, C12, and C44 in consecutive columns.
|
||||
|
||||
""" + string.replace('$Id$','\n','\\n')
|
||||
""", version = string.replace(scriptID,'\n','\\n')
|
||||
)
|
||||
|
||||
parser.add_option('-c','--stiffness', dest='vector', action='extend', type='string', \
|
||||
help='heading of column containing C11 (followed by C12, C44) field values', \
|
||||
metavar='<label>')
|
||||
parser.add_option('-c','--stiffness', dest='vector', action='extend', type='string', metavar='<string LIST>', \
|
||||
help='heading of column containing C11 (followed by C12, C44) field values')
|
||||
parser.add_option('-d','--direction', \
|
||||
'--hkl', dest='hkl', action='store', type='int', nargs=3, \
|
||||
'--hkl', dest='hkl', action='store', type='int', nargs=3, metavar='int int int', \
|
||||
help='direction of elastic modulus %default')
|
||||
|
||||
parser.set_defaults(vector = [])
|
||||
parser.set_defaults(hkl = [1,1,1])
|
||||
|
||||
|
|
@ -72,9 +56,7 @@ datainfo = { # lis
|
|||
'label':[]},
|
||||
}
|
||||
|
||||
|
||||
if options.vector != None: datainfo['vector']['label'] += options.vector
|
||||
|
||||
datainfo['vector']['label'] += options.vector
|
||||
|
||||
# ------------------------------------------ setup file handles ---------------------------------------
|
||||
|
||||
|
|
@ -87,19 +69,16 @@ else:
|
|||
files.append({'name':name, 'input':open(name), 'output':open(name+'_tmp','w'), 'croak':sys.stderr})
|
||||
|
||||
# ------------------------------------------ loop over input files ---------------------------------------
|
||||
|
||||
for file in files:
|
||||
if file['name'] != 'STDIN': file['croak'].write(file['name']+'\n')
|
||||
if file['name'] != 'STDIN': file['croak'].write('\033[1m'+scriptName+'\033[0m: '+file['name']+'\n')
|
||||
else: file['croak'].write('\033[1m'+scriptName+'\033[0m\n')
|
||||
|
||||
table = damask.ASCIItable(file['input'],file['output'],False) # make unbuffered ASCII_table
|
||||
table.head_read() # read ASCII header info
|
||||
table.info_append(string.replace('$Id$','\n','\\n') + \
|
||||
'\t' + ' '.join(sys.argv[1:]))
|
||||
table = damask.ASCIItable(file['input'],file['output'],False) # make unbuffered ASCII_table
|
||||
table.head_read() # read ASCII header info
|
||||
table.info_append(string.replace(scriptID,'\n','\\n') + '\t' + ' '.join(sys.argv[1:]))
|
||||
|
||||
# --------------- figure out columns to process
|
||||
active = {}
|
||||
column = {}
|
||||
head = []
|
||||
active = defaultdict(list)
|
||||
column = defaultdict(dict)
|
||||
|
||||
for datatype,info in datainfo.items():
|
||||
for label in info['label']:
|
||||
|
|
@ -107,36 +86,33 @@ for file in files:
|
|||
for key in ['1_'+label,label]:
|
||||
if key in table.labels:
|
||||
foundIt = True
|
||||
if datatype not in active: active[datatype] = []
|
||||
if datatype not in column: column[datatype] = {}
|
||||
active[datatype].append(label)
|
||||
column[datatype][label] = table.labels.index(key) # remember columns of requested data
|
||||
table.labels_append('E%i%i%i(%s)'%(options.hkl[0],
|
||||
options.hkl[1],
|
||||
options.hkl[2],label)) # extend ASCII header with new labels
|
||||
column[datatype][label] = table.labels.index(key) # remember columns of requested data
|
||||
if not foundIt:
|
||||
file['croak'].write('column %s not found...\n'%label)
|
||||
|
||||
# ------------------------------------------ assemble header ---------------------------------------
|
||||
file['croak'].write('column %s not found...\n'%label)
|
||||
|
||||
# ------------------------------------------ assemble header ---------------------------------------
|
||||
for datatype,labels in active.items(): # loop over vector,tensor
|
||||
for label in labels: # loop over all requested stiffnesses
|
||||
table.labels_append('E%i%i%i(%s)'%(options.hkl[0],
|
||||
options.hkl[1],
|
||||
options.hkl[2],label)) # extend ASCII header with new labels
|
||||
table.head_write()
|
||||
|
||||
# ------------------------------------------ process data ---------------------------------------
|
||||
|
||||
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 stiffnesses
|
||||
# ------------------------------------------ process data ----------------------------------------
|
||||
outputAlive = True
|
||||
while outputAlive and 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 stiffnesses
|
||||
table.data_append(E_hkl(map(float,table.data[column[datatype][label]:\
|
||||
column[datatype][label]+datainfo[datatype]['len']]),options.hkl))
|
||||
|
||||
table.data_write() # output processed line
|
||||
outputAlive = table.data_write() # output processed line
|
||||
|
||||
# ------------------------------------------ output result ---------------------------------------
|
||||
outputAlive and table.output_flush() # just in case of buffered ASCII table
|
||||
|
||||
table.output_flush() # just in case of buffered ASCII table
|
||||
|
||||
file['input'].close() # close input ASCII table (works for stdin)
|
||||
file['output'].close() # close output ASCII table (works for stdout)
|
||||
if file['name'] != 'STDIN':
|
||||
file['input'].close() # close input ASCII table
|
||||
file['output'].close() # close output ASCII table
|
||||
os.rename(file['name']+'_tmp',file['name']) # overwrite old one with tmp new
|
||||
os.rename(file['name']+'_tmp',file['name']) # overwrite old one with tmp new
|
||||
|
|
|
|||
Loading…
Reference in New Issue