more and improved tests for add...
This commit is contained in:
Martin Diehl
parent
38048a09f2
commit
7954c9a4a3
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@ -103,10 +103,8 @@ for file in files:
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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.labels_append({True:['%i_%s'%(i+1,label) for i in xrange(labelLen[label])],
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False:label}[labelLen[label]>1] )
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table.head_write()
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firstLine = False
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@ -124,10 +124,8 @@ for file in files:
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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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for accuracy in options.accuracy:
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if datatype == 'vector': # extend ASCII header with new labels
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table.labels_append(['div%s(%s)'%(accuracy,label)])
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if datatype == 'tensor':
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table.labels_append(['%i_div%s(%s)'%(i+1,accuracy,label) for i in xrange(3)])
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table.labels_append({False: ['%i_div%s(%s)'%(i+1,accuracy,label) for i in xrange(3)], # extend ASCII header with new labels
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{True: ['div%s(%s)'%(accuracy,label)]} [datatype == 'tensor'])
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table.head_write()
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# ------------------------------------------ read value field --------------------------------------
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@ -20,32 +20,32 @@ Add RGB color value corresponding to TSL-OIM scheme for inverse pole figures.
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""", version = string.replace(scriptID,'\n','\\n')
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)
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parser.add_option('-p', '--pole', dest='pole', type='float', nargs=3, metavar='X Y Z',
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parser.add_option('-p', '--pole', dest='pole', action='store', type='float', nargs=3, metavar='float float float',
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help = 'lab frame direction for inverse pole figure %default')
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parser.add_option('-s', '--symmetry', dest='symmetry', type='string',
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help = 'crystal symmetry [%default]')
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parser.add_option('-e', '--eulers', dest='eulers', type='string', metavar='LABEL',
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parser.add_option('-s', '--symmetry', dest='symmetry', action='store', type='choice',
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choices=damask.Symmetry.lattices[1:], metavar='string',
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help = 'crystal symmetry (%s) [cubic]'%(', '.join(damask.Symmetry.lattices[1:])))
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parser.add_option('-e', '--eulers', dest='eulers', action='store', type='string', metavar='string',
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help = 'Euler angles label')
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parser.add_option('-d', '--degrees', dest='degrees', action='store_true',
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help = 'Euler angles are given in degrees [%default]')
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parser.add_option('-m', '--matrix', dest='matrix', type='string', metavar='LABEL',
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parser.add_option('-m', '--matrix', dest='matrix', action='store', type='string', metavar='string',
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help = 'orientation matrix label')
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parser.add_option('-a', dest='a', type='string', metavar='LABEL',
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parser.add_option('-a', dest='a', action='store', type='string', metavar='string',
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help = 'crystal frame a vector label')
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parser.add_option('-b', dest='b', type='string', metavar='LABEL',
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parser.add_option('-b', dest='b', action='store', type='string', metavar='string',
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help = 'crystal frame b vector label')
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parser.add_option('-c', dest='c', type='string', metavar='LABEL',
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parser.add_option('-c', dest='c', action='store', type='string', metavar='string',
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help = 'crystal frame c vector label')
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parser.add_option('-q', '--quaternion', dest='quaternion', type='string', metavar='LABEL',
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parser.add_option('-q', '--quaternion', dest='quaternion', action='store', type='string', metavar='string',
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help = 'quaternion label')
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parser.set_defaults(pole = [0.0,0.0,1.0])
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parser.set_defaults(symmetry = 'cubic')
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parser.set_defaults(degrees = False)
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(options, filenames) = parser.parse_args()
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datainfo = { # list of requested labels per datatype
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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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'vector': {'len':3,
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@ -61,12 +61,11 @@ if options.a != None and \
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if options.matrix != None: datainfo['tensor']['label'] += [options.matrix]; input = 'matrix'
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if options.quaternion != None: datainfo['quaternion']['label'] += [options.quaternion]; input = 'quaternion'
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toRadians = math.pi/180.0 if options.degrees else 1.0 # rescale degrees to radians
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toRadians = math.pi/180.0 if options.degrees else 1.0 # rescale degrees to radians
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pole = np.array(options.pole)
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pole /= np.linalg.norm(pole)
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# ------------------------------------------ setup file handles ---------------------------------------
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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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@ -75,16 +74,15 @@ else:
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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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# ------------------------------------------ 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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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 = 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 columns to process
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active = defaultdict(list)
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column = defaultdict(dict)
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@ -95,36 +93,33 @@ for file in files:
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if key in table.labels:
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foundIt = True
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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[datatype][label] = table.labels.index(key) # remember columns of requested data
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if not foundIt:
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file['croak'].write('column %s not found...\n'%label)
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break
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table.labels_append(['%i_IPF_%g%g%g'%(i+1,options.pole[0],options.pole[1],options.pole[2]) for i in xrange(3)])
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# ------------------------------------------ assemble header ---------------------------------------
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table.labels_append(['%i_IPF_%g%g%g'%(i+1,options.pole[0],options.pole[1],options.pole[2]) for i in xrange(3)])
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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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# ------------------------------------------ process data ----------------------------------------
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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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if input == 'eulers':
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o = damask.Orientation(Eulers=toRadians*np.array(map(float,table.data[column['vector'][options.eulers]:\
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column['vector'][options.eulers]+datainfo['vector']['len']])),
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column['vector'][options.eulers]+datainfo['vector']['len']])),
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symmetry=options.symmetry).reduced()
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elif input == 'matrix':
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o = damask.Orientation(matrix=np.array([map(float,table.data[column['tensor'][options.matrix]:\
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column['tensor'][options.matrix]+datainfo['tensor']['len']])]),
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column['tensor'][options.matrix]+datainfo['tensor']['len']])]),
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symmetry=options.symmetry).reduced()
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elif input == 'frame':
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o = damask.Orientation(matrix=np.array([map(float,table.data[column['vector'][options.a]:\
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column['vector'][options.a]+datainfo['vector']['len']] + \
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table.data[column['vector'][options.b]:\
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column['vector'][options.b]+datainfo['vector']['len']] + \
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table.data[column['vector'][options.c]:\
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column['vector'][options.c]+datainfo['vector']['len']]
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column['vector'][options.a]+datainfo['vector']['len']] + \
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table.data[column['vector'][options.b]:\
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column['vector'][options.b]+datainfo['vector']['len']] + \
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table.data[column['vector'][options.c]:\
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column['vector'][options.c]+datainfo['vector']['len']]
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)]).reshape(3,3),
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symmetry=options.symmetry).reduced()
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elif input == 'quaternion':
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@ -1,57 +1,37 @@
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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,damask
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from optparse import OptionParser, Option
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import os,re,sys,math,string
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from optparse import OptionParser
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import damask
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scriptID = '$Id: addNorm.py 3167 2014-06-06 09:43:28Z p.eisenlohr $'
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scriptID = '$Id: addCauchy.py 3301 2014-07-22 14:21:49Z MPIE\m.diehl $'
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scriptName = scriptID.split()[1]
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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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parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
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Add data in column(s) of second ASCIItable selected from row that is given by the value in a mapping column.
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""" + string.replace(scriptID,'\n','\\n')
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""", version = string.replace(scriptID,'\n','\\n')
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)
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parser.add_option('-a','--asciitable', dest='asciitable', type='string', metavar='FILE',
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parser.add_option('-a','--asciitable', dest='asciitable', action='store', type='string', metavar='string',
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help='mapped ASCIItable')
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parser.add_option('-c','--map', dest='map', action='store', type='string', metavar='string',
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help='heading of column containing row mapping')
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parser.add_option('-c','--map', dest='map', type='string', metavar='LABEL',
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help='heading of column containing row mapping')
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parser.add_option('-o','--offset', dest='offset', type='int', metavar='n',
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parser.add_option('-o','--offset', dest='offset', action='store', type='int', metavar='int',
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help='offset between mapped column value and row')
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parser.add_option('-v','--vector', dest='vector', action='extend', type='string', metavar='LABEL',
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parser.add_option('-v','--vector', dest='vector', action='extend', type='string', metavar='<string LIST>',
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help='heading of columns containing vector field values')
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parser.add_option('-t','--tensor', dest='tensor', action='extend', type='string', metavar='LABEL',
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parser.add_option('-t','--tensor', dest='tensor', action='extend', type='string', metavar='<string LIST>',
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help='heading of columns containing tensor field values')
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parser.add_option('-s','--special', dest='special', action='extend', type='string', metavar='LABEL',
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parser.add_option('-s','--special', dest='special', action='extend', type='string', metavar='<string LIST>',
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help='heading of columns containing field values of special dimension')
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parser.add_option('-d','--dimension', dest='N', action='store', type='int', \
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parser.add_option('-d','--dimension', dest='N', action='store', type='int', metavar='int',
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help='dimension of special field values [%default]')
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parser.set_defaults(vector = [])
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parser.set_defaults(tensor = [])
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parser.set_defaults(special = [])
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@ -62,8 +42,10 @@ parser.set_defaults(N = 1)
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if len(options.vector) + len(options.tensor) + len(options.special) == 0:
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parser.error('no data column specified...')
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if options.map == None:
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parser.error('missing mapping column...')
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datainfo = { # list of requested labels per datatype
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datainfo = { # list of requested labels per datatype
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'vector': {'len':3,
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'label':[]},
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'tensor': {'len':9,
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@ -72,14 +54,14 @@ datainfo = { # lis
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'label':[]},
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}
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if options.vector != None: datainfo['vector']['label'] += options.vector
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if options.tensor != None: datainfo['tensor']['label'] += options.tensor
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if options.special != None: datainfo['special']['label'] += options.special
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# ------------------------------------------ processing mapping ASCIItable ---------------------------
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if options.asciitable != None and os.path.isfile(options.asciitable):
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mappedTable = damask.ASCIItable(open(options.asciitable),open(options.asciitable),False)
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mappedTable.head_read() # read ASCII header info of mapped table
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mappedTable = damask.ASCIItable(open(options.asciitable),None,False)
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mappedTable.head_read() # read ASCII header info of mapped table
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labels = []
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indices = []
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@ -90,7 +72,7 @@ if options.asciitable != None and os.path.isfile(options.asciitable):
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for key in ['1_'+label,label]:
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if key in mappedTable.labels:
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foundIt = True
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labels.append(label) # extend labels
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labels.append(label) # extend labels
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indices += range(mappedTable.labels.index(key),
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mappedTable.labels.index(key)+datainfo[datatype]['len'])
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if not foundIt:
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@ -98,18 +80,11 @@ if options.asciitable != None and os.path.isfile(options.asciitable):
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break
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mappedTable.data_readArray(indices)
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mappedTable.input_close() # close mapped input ASCII table
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mappedTable.output_close() # close mapped output (same as input) ASCII table
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mappedTable.__IO__['in'].close() # close mapped input ASCII table
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else:
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parser.error("Missing mapped ASCIItable")
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if options.map == None:
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parser.error("Missing mapping column")
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# ------------------------------------------ setup file handles ---------------------------------------
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parser.error('missing mapped ASCIItable...')
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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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@ -118,43 +93,37 @@ else:
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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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# ------------------------------------------ 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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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 = 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 columns to process
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if options.map not in table.labels:
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file['croak'].write('column %s not found...\n'%options.map)
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continue
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mappedColumn = table.labels.index(options.map)
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for label in labels:
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table.labels_append(label) # extend ASCII header of current table with new labels
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# ------------------------------------------ assemble header ---------------------------------------
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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({True:['%i_%s'%(i+1,label) for i in xrange(info['len'])],
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False:table.labels_append(label)}[info['len']>1] ) # extend ASCII header of current table 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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mappedColumn = table.labels.index(options.map)
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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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# file['croak'].write('%i\n'%(int(table.data[mappedColumn])+options.offset-1))
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table.data_append(mappedTable.data[int(table.data[mappedColumn])+options.offset-1]) # add all mapped data types
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outputAlive = table.data_write() # output processed line
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while outputAlive and table.data_read(): # read next data line of ASCII table
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table.data_append(mappedTable.data[int(table.data[mappedColumn])+options.offset-1]) # add all mapped data types
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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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outputAlive and table.output_flush() # just in case of buffered ASCII table
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table.input_close() # close input 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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table.output_close() # close output ASCII table
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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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@ -3,6 +3,7 @@
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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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@ -26,15 +27,13 @@ def Mises(what,tensor):
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parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
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Add vonMises equivalent values for symmetric part of requested strains and/or stresses.
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""" + string.replace(scriptID,'\n','\\n')
|
||||
""", version = string.replace(scriptID,'\n','\\n')
|
||||
)
|
||||
|
||||
|
||||
parser.add_option('-e','--strain', dest='strain', action='extend', type='string', \
|
||||
help='heading(s) of columns containing strain tensors')
|
||||
parser.add_option('-s','--stress', dest='stress', action='extend', type='string', \
|
||||
help='heading(s) of columns containing stress tensors')
|
||||
|
||||
parser.add_option('-e','--strain', dest='strain', action='extend', type='string', metavar='<string LIST>',
|
||||
help='heading(s) of columns containing strain tensors')
|
||||
parser.add_option('-s','--stress', dest='stress', action='extend', type='string', metavar='<string LIST>',
|
||||
help='heading(s) of columns containing stress tensors')
|
||||
parser.set_defaults(strain = [])
|
||||
parser.set_defaults(stress = [])
|
||||
|
||||
|
|
@ -43,19 +42,17 @@ parser.set_defaults(stress = [])
|
|||
if len(options.strain) + len(options.stress) == 0:
|
||||
parser.error('no data column specified...')
|
||||
|
||||
datainfo = { # list of requested labels per datatype
|
||||
datainfo = { # list of requested labels per datatype
|
||||
'strain': {'len':9,
|
||||
'label':[]},
|
||||
'stress': {'len':9,
|
||||
'label':[]},
|
||||
}
|
||||
|
||||
|
||||
if options.strain != None: datainfo['strain']['label'] += options.strain
|
||||
if options.stress != None: datainfo['stress']['label'] += options.stress
|
||||
|
||||
# ------------------------------------------ setup file handles ---------------------------------------
|
||||
|
||||
files = []
|
||||
if filenames == []:
|
||||
files.append({'name':'STDIN', 'input':sys.stdin, 'output':sys.stdout, 'croak':sys.stderr})
|
||||
|
|
@ -64,55 +61,48 @@ else:
|
|||
if os.path.exists(name):
|
||||
files.append({'name':name, 'input':open(name), 'output':open(name+'_tmp','w'), 'croak':sys.stderr})
|
||||
|
||||
# ------------------------------------------ loop over input files ---------------------------------------
|
||||
|
||||
# ------------------------------------------ loop over input files ---------------------------------------
|
||||
for file in files:
|
||||
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 = 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('Mises(%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('Mises(%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
|
||||
# ------------------------------------------ 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 norms
|
||||
table.data_append(Mises(datatype,
|
||||
np.array(map(float,table.data[column[datatype][label]:
|
||||
column[datatype][label]+datainfo[datatype]['len']]),'d').reshape(3,3)))
|
||||
|
||||
table.data_write() # output processed line
|
||||
np.array(map(float,table.data[column[datatype][label]:
|
||||
column[datatype][label]+datainfo[datatype]['len']]),'d').reshape(3,3)))
|
||||
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
|
||||
|
|
|
|||
|
|
@ -1,71 +1,45 @@
|
|||
#!/usr/bin/env python
|
||||
# -*- coding: UTF-8 no BOM -*-
|
||||
|
||||
import os,re,sys,math,string,damask
|
||||
import os,re,sys,math,string
|
||||
from collections import defaultdict
|
||||
from optparse import OptionParser, Option
|
||||
from optparse import OptionParser
|
||||
import damask
|
||||
|
||||
scriptID = '$Id$'
|
||||
scriptName = scriptID.split()[1]
|
||||
|
||||
# -----------------------------
|
||||
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)
|
||||
|
||||
|
||||
|
||||
# definition of element-wise p-norms for matrices
|
||||
|
||||
# p = 1
|
||||
def normAbs(object):
|
||||
def normAbs(object): # p = 1
|
||||
return sum(map(abs, object))
|
||||
|
||||
# p = 2
|
||||
def normFrobenius(object):
|
||||
def normFrobenius(object): # p = 2
|
||||
return math.sqrt(sum([x*x for x in object]))
|
||||
|
||||
# p = infinity
|
||||
def normMax(object):
|
||||
def normMax(object): # p = infinity
|
||||
return max(map(abs, object))
|
||||
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
# 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 norm of requested column(s) being either vectors or tensors.
|
||||
|
||||
""" + string.replace(scriptID,'\n','\\n')
|
||||
""", version = string.replace(scriptID,'\n','\\n')
|
||||
)
|
||||
|
||||
normChoices = ['abs','frobenius','max']
|
||||
|
||||
parser.add_option('-n','--norm', dest='norm', action='store', type='choice', choices=normChoices, \
|
||||
help='type of element-wise p-norm (%s) [2]'%(','.join(map(str,normChoices))))
|
||||
parser.add_option('-v','--vector', dest='vector', action='extend', type='string', \
|
||||
parser.add_option('-n','--norm', dest='norm', action='store', type='choice', choices=normChoices, metavar='string',
|
||||
help='type of element-wise p-norm (%s) [frobenius]'%(','.join(map(str,normChoices))))
|
||||
parser.add_option('-v','--vector', dest='vector', action='extend', type='string', metavar='<string LIST>',
|
||||
help='heading of columns containing vector field values')
|
||||
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','--special', dest='special', action='extend', type='string', \
|
||||
parser.add_option('-s','--special', dest='special', action='extend', type='string', metavar='<string LIST>',
|
||||
help='heading of columns containing field values of special dimension')
|
||||
parser.add_option('-d','--dimension', dest='N', action='store', type='int', \
|
||||
parser.add_option('-d','--dimension', dest='N', action='store', type='int', metavar='int',
|
||||
help='dimension of special field values [%default]')
|
||||
|
||||
parser.set_defaults(norm = 'frobenius')
|
||||
parser.set_defaults(vector = [])
|
||||
parser.set_defaults(tensor = [])
|
||||
|
|
@ -77,7 +51,7 @@ parser.set_defaults(N = 12)
|
|||
if len(options.vector) + len(options.tensor) + len(options.special)== 0:
|
||||
parser.error('no data column specified...')
|
||||
|
||||
datainfo = { # list of requested labels per datatype
|
||||
datainfo = { # list of requested labels per datatype
|
||||
'vector': {'len':3,
|
||||
'label':[]},
|
||||
'tensor': {'len':9,
|
||||
|
|
@ -86,14 +60,11 @@ datainfo = { # lis
|
|||
'label':[]},
|
||||
}
|
||||
|
||||
|
||||
if options.vector != None: datainfo['vector']['label'] += options.vector
|
||||
if options.tensor != None: datainfo['tensor']['label'] += options.tensor
|
||||
if options.special != None: datainfo['special']['label'] += options.special
|
||||
|
||||
|
||||
# ------------------------------------------ setup file handles ---------------------------------------
|
||||
|
||||
files = []
|
||||
if filenames == []:
|
||||
files.append({'name':'STDIN', 'input':sys.stdin, 'output':sys.stdout, 'croak':sys.stderr})
|
||||
|
|
@ -107,48 +78,41 @@ for file in files:
|
|||
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 = 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 = defaultdict(list)
|
||||
column = defaultdict(dict)
|
||||
|
||||
for datatype,info in datainfo.items():
|
||||
for label in info['label']:
|
||||
foundIt = False
|
||||
for key in ['1_'+label,label]:
|
||||
if key in table.labels:
|
||||
foundIt = True
|
||||
active[datatype].append(label)
|
||||
column[datatype][label] = table.labels.index(key) # remember columns of requested data
|
||||
table.labels_append('norm%s(%s)'%(options.norm.capitalize(),label)) # extend ASCII header with new labels
|
||||
if not foundIt:
|
||||
file['croak'].write('column %s not found...\n'%label)
|
||||
break
|
||||
|
||||
# ------------------------------------------ assemble header ---------------------------------------
|
||||
key = {True :'1_%s',
|
||||
False:'%s' }[info['len']>1]%label
|
||||
if key not in table.labels:
|
||||
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
|
||||
|
||||
# ------------------------------------------ assemble header ---------------------------------------
|
||||
for datatype,labels in active.items(): # loop over vector,tensor
|
||||
for label in labels: # loop over all requested determinants
|
||||
table.labels_append('norm%s(%s)'%(options.norm.capitalize(),label)) # extend ASCII header with new labels
|
||||
table.head_write()
|
||||
|
||||
# ------------------------------------------ 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 norms
|
||||
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 norms
|
||||
eval("table.data_append(norm%s(map(float,table.data[column[datatype][label]:column[datatype][label]+datainfo[datatype]['len']])))"%options.norm.capitalize())
|
||||
|
||||
outputAlive = 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
|
||||
|
||||
outputAlive and 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
|
||||
|
|
|
|||
|
|
@ -2,60 +2,47 @@
|
|||
# -*- coding: UTF-8 no BOM -*-
|
||||
|
||||
import os,sys,string,itertools,re,math,numpy
|
||||
import damask
|
||||
from collections import defaultdict
|
||||
from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
|
||||
from optparse import OptionParser
|
||||
import damask
|
||||
|
||||
scriptID = '$Id$'
|
||||
scriptName = scriptID.split()[1]
|
||||
|
||||
#--------------------------------------------------------------------------------------------------
|
||||
class extendedOption(Option):
|
||||
#--------------------------------------------------------------------------------------------------
|
||||
# used for definition of new option parser action 'extend', which enables to take multiple option arguments
|
||||
# taken from online tutorial http://docs.python.org/library/optparse.html
|
||||
|
||||
ACTIONS = Option.ACTIONS + ("extend",)
|
||||
STORE_ACTIONS = Option.STORE_ACTIONS + ("extend",)
|
||||
TYPED_ACTIONS = Option.TYPED_ACTIONS + ("extend",)
|
||||
ALWAYS_TYPED_ACTIONS = Option.ALWAYS_TYPED_ACTIONS + ("extend",)
|
||||
# --------------------------------------------------------------------
|
||||
# MAIN
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
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)
|
||||
|
||||
|
||||
parser = OptionParser(option_class=extendedOption, usage='%prog options [file[s]]', description = """\
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
|
||||
Add quaternion and/or Bunge Euler angle representation of crystal lattice orientation.
|
||||
Orientation is given by quaternion, Euler angles,
|
||||
rotation matrix, or crystal frame coordinates (i.e. component vectors of rotation matrix).
|
||||
""" + string.replace(scriptID,'\n','\\n')
|
||||
|
||||
""", version = string.replace(scriptID,'\n','\\n')
|
||||
)
|
||||
|
||||
parser.add_option('-o', '--output', dest='output', action='append', metavar='<LIST>',
|
||||
help = 'output orientation formats')
|
||||
parser.add_option('-s', '--symmetry', dest='symmetry', type='string',
|
||||
help = 'crystal symmetry [%default]')
|
||||
parser.add_option('-r', '--rotation', dest='rotation', type='float', nargs=4,
|
||||
help = 'angle and axis to (pre)rotate orientation')
|
||||
parser.add_option('-e', '--eulers', dest='eulers', type='string', metavar='LABEL',
|
||||
help = 'Euler angles')
|
||||
parser.add_option('-d', '--degrees', dest='degrees', action='store_true',
|
||||
help = 'Angles are given in degrees [%default]')
|
||||
parser.add_option('-m', '--matrix', dest='matrix', type='string', metavar='LABEL',
|
||||
help = 'orientation matrix')
|
||||
parser.add_option('-a', dest='a', type='string', metavar='LABEL',
|
||||
help = 'crystal frame a vector')
|
||||
parser.add_option('-b', dest='b', type='string', metavar='LABEL',
|
||||
help = 'crystal frame b vector')
|
||||
parser.add_option('-c', dest='c', type='string', metavar='LABEL',
|
||||
help = 'crystal frame c vector')
|
||||
parser.add_option('-q', '--quaternion', dest='quaternion', type='string', metavar='LABEL',
|
||||
help = 'quaternion')
|
||||
|
||||
outputChoices = ['quaternion','eulers']
|
||||
parser.add_option('-o', '--output', dest='output', action='extend', type='string', metavar='<string LIST>',
|
||||
help = 'output orientation formats (%s)'%(','.join(outputChoices)))
|
||||
parser.add_option('-s', '--symmetry', dest='symmetry', action='store', type='choice',
|
||||
choices=damask.Symmetry.lattices[1:], metavar='string',
|
||||
help = 'crystal symmetry (%s) [cubic]'%(', '.join(damask.Symmetry.lattices[1:])))
|
||||
parser.add_option('-r', '--rotation', dest='rotation', action='store', type='float', nargs=4, metavar='float float float float',
|
||||
help = 'angle and axis to (pre)rotate orientation')
|
||||
parser.add_option('-e', '--eulers', dest='eulers', action='store', type='string', metavar='string',
|
||||
help = 'Euler angles label')
|
||||
parser.add_option('-d', '--degrees', dest='degrees', action='store_true',
|
||||
help = 'Euler angles are given in degrees [%default]')
|
||||
parser.add_option('-m', '--matrix', dest='matrix', action='store', type='string', metavar='string',
|
||||
help = 'orientation matrix label')
|
||||
parser.add_option('-a', dest='a', action='store', type='string', metavar='string',
|
||||
help = 'crystal frame a vector label')
|
||||
parser.add_option('-b', dest='b', action='store', type='string', metavar='string',
|
||||
help = 'crystal frame b vector label')
|
||||
parser.add_option('-c', dest='c', action='store', type='string', metavar='string',
|
||||
help = 'crystal frame c vector label')
|
||||
parser.add_option('-q', '--quaternion', dest='quaternion', action='store', type='string', metavar='string',
|
||||
help = 'quaternion label')
|
||||
parser.set_defaults(output = [])
|
||||
parser.set_defaults(symmetry = 'cubic')
|
||||
parser.set_defaults(rotation = [0.,1.,1.,1.]) # no rotation about 1,1,1
|
||||
|
|
@ -72,6 +59,9 @@ datainfo = { # lis
|
|||
'label':[]},
|
||||
}
|
||||
|
||||
if not set(options.output).issubset(set(outputChoices)):
|
||||
parser.error('output must be chosen from %s...'%(', '.join(outputChoices)))
|
||||
|
||||
if options.eulers != None: datainfo['vector']['label'] += [options.eulers]; input = 'eulers'
|
||||
if options.a != None and \
|
||||
options.b != None and \
|
||||
|
|
@ -94,16 +84,15 @@ else:
|
|||
if os.path.exists(name):
|
||||
files.append({'name':name, 'input':open(name), 'output':open(name+'_tmp','w'), 'croak':sys.stderr})
|
||||
|
||||
#--- loop over input files ------------------------------------------------------------------------
|
||||
# ------------------------------------------ loop over input files ----------------------------------
|
||||
for file in files:
|
||||
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'],buffered = False) # make unbuffered ASCII_table
|
||||
table.head_read() # read ASCII header info
|
||||
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 = defaultdict(list)
|
||||
column = defaultdict(dict)
|
||||
|
||||
|
|
@ -114,25 +103,22 @@ for file in files:
|
|||
if key in table.labels:
|
||||
foundIt = True
|
||||
active[datatype].append(label)
|
||||
column[datatype][label] = table.labels.index(key) # remember columns of requested data
|
||||
column[datatype][label] = table.labels.index(key) # remember columns of requested data
|
||||
if not foundIt:
|
||||
file['croak'].write('column %s not found...\n'%label)
|
||||
break
|
||||
|
||||
# ------------------------------------------ assemble header ---------------------------------------
|
||||
for output in options.output:
|
||||
if output == 'quaternion':
|
||||
table.labels_append(['%i_quaternion_%s'%(i+1,options.symmetry) for i in xrange(4)])
|
||||
if output == 'eulers':
|
||||
table.labels_append(['%i_eulers_%s'%(i+1,options.symmetry) for i in xrange(3)])
|
||||
|
||||
# ------------------------------------------ assemble header ---------------------------------------
|
||||
|
||||
table.head_write()
|
||||
|
||||
# ------------------------------------------ process data ---------------------------------------
|
||||
|
||||
while table.data_read(): # read next data line of ASCII table
|
||||
|
||||
# ------------------------------------------ process data ----------------------------------------
|
||||
outputAlive = True
|
||||
while outputAlive and table.data_read(): # read next data line of ASCII table
|
||||
if input == 'eulers':
|
||||
o = damask.Orientation(Eulers=toRadians*numpy.array(map(float,table.data[column['vector'][options.eulers]:\
|
||||
column['vector'][options.eulers]+datainfo['vector']['len']])),
|
||||
|
|
@ -155,7 +141,6 @@ for file in files:
|
|||
column['quaternion'][options.quaternion]+datainfo['quaternion']['len']])),
|
||||
symmetry=options.symmetry).reduced()
|
||||
|
||||
|
||||
o.quaternion = r*o.quaternion
|
||||
|
||||
for output in options.output:
|
||||
|
|
@ -163,14 +148,12 @@ for file in files:
|
|||
table.data_append(o.asQuaternion())
|
||||
if output == 'eulers':
|
||||
table.data_append(o.asEulers('Bunge'))
|
||||
|
||||
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