new ASCIItable scripts to add
- quaternion and/or Euler representation of lattice orientation (given in rotation matrix, etc.) - RGB color code of crystal direction in laboratory frame (matching closely the TSL-OIM scheme of inverse pole figures).
This commit is contained in:
Philip Eisenlohr
parent
d17d6636df
commit
a45c7dbb62
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@ -0,0 +1,156 @@
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#!/usr/bin/env python
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import os,sys,string,re,math,numpy
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import damask
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from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
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scriptID = '$Id$'
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scriptName = scriptID.split()[1]
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#--------------------------------------------------------------------------------------------------
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class extendedOption(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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parser = OptionParser(option_class=extendedOption, usage='%prog options [file[s]]', description = """
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Add RGB color value corresponding to TSL-OIM scheme for inverse pole figures.
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""" + string.replace(scriptID,'\n','\\n')
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)
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parser.add_option('-p', '--pole', dest='pole', type='float', nargs=3,\
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help = 'list of poles (directions)')
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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', \
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help = 'Euler angles label')
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parser.add_option('-m', '--matrix', dest='matrix', type='string', \
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help = 'orientation matrix label')
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parser.add_option('-a', dest='a', type='string', \
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help = 'crystal frame a vector label')
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parser.add_option('-b', dest='b', type='string', \
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help = 'crystal frame b vector label')
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parser.add_option('-c', dest='c', type='string', \
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help = 'crystal frame c vector label')
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parser.add_option('-q', '--quaternion', dest='quaternion', type='string', \
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help = 'quaternion label')
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parser.set_defaults(output = [])
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parser.set_defaults(symmetry = 'cubic')
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(options, filenames) = parser.parse_args()
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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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'label':[]},
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'quaternion': {'len':4,
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'label':[]},
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}
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if options.eulers != None: datainfo['vector']['label'] += [options.eulers]; input = 'eulers'
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if options.a != None and \
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options.b != None and \
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options.c != None: datainfo['vector']['label'] += [options.a,options.b,options.c]; input = 'frame'
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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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pole = numpy.array(options.pole)
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pole /= numpy.linalg.norm(pole)
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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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#--- 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.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 = {}
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column = {}
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head = []
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for datatype,info in datainfo.items():
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for label in info['label']:
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foundIt = False
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for key in ['1_'+label,label]:
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if key in table.labels:
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foundIt = True
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if datatype not in active: active[datatype] = []
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if datatype not in column: column[datatype] = {}
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active[datatype].append(label)
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column[datatype][label] = table.labels.index(key) # remember columns of requested data
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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.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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if input == 'eulers':
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o = damask.Orientation(Eulers=numpy.array(map(float,table.data[column['vector'][options.eulers]:\
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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=numpy.array([map(float,table.data[column['tensor'][options.matrix]:\
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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=numpy.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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)]).reshape(3,3),
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symmetry=options.symmetry).reduced()
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elif input == 'quaternion':
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o = damask.Orientation(quaternion=numpy.array(map(float,table.data[column['quaternion'][options.quaternion]:\
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column['quaternion'][options.quaternion]+datainfo['quaternion']['len']])),
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symmetry=options.symmetry).reduced()
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table.data_append(o.IPFcolor(pole))
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table.data_write() # output processed line
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# ------------------------------------------ output result ---------------------------------------
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table.output_flush() # just in case of buffered ASCII table
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if file['name'] != 'STDIN':
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file['input'].close() # close input ASCII table
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file['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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@ -0,0 +1,165 @@
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#!/usr/bin/env python
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import os,sys,string,itertools,re,math,numpy
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import damask
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from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
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scriptID = '$Id$'
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scriptName = scriptID.split()[1]
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#--------------------------------------------------------------------------------------------------
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class extendedOption(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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parser = OptionParser(option_class=extendedOption, usage='%prog options [file[s]]', description = """
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Add quaternion and/or Bunge Euler angle representation of crystal lattice orientation.
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Orientation is given by quaternion, Euler angles,
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rotation matrix, or crystal frame coordinates (i.e. component vectors of rotation matrix).
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""" + string.replace(scriptID,'\n','\\n')
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)
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parser.add_option('-o', '--orientations', dest='output', action='append', \
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help = 'list of output orientation formats')
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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', \
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help = 'Euler angles label')
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parser.add_option('-m', '--matrix', dest='matrix', type='string', \
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help = 'orientation matrix label')
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parser.add_option('-a', dest='a', type='string', \
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help = 'crystal frame a vector label')
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parser.add_option('-b', dest='b', type='string', \
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help = 'crystal frame b vector label')
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parser.add_option('-c', dest='c', type='string', \
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help = 'crystal frame c vector label')
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parser.add_option('-q', '--quaternion', dest='quaternion', type='string', \
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help = 'quaternion label')
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parser.set_defaults(output = [])
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parser.set_defaults(symmetry = 'cubic')
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(options, filenames) = parser.parse_args()
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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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'label':[]},
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'quaternion': {'len':4,
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'label':[]},
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}
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if options.eulers != None: datainfo['vector']['label'] += [options.eulers]; input = 'eulers'
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if options.a != None and \
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options.b != None and \
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options.c != None: datainfo['vector']['label'] += [options.a,options.b,options.c]; input = 'frame'
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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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options.output = map(lambda x: x.lower(), options.output)
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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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#--- 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.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 = {}
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column = {}
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head = []
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for datatype,info in datainfo.items():
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for label in info['label']:
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foundIt = False
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for key in ['1_'+label,label]:
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if key in table.labels:
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foundIt = True
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if datatype not in active: active[datatype] = []
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if datatype not in column: column[datatype] = {}
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active[datatype].append(label)
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column[datatype][label] = table.labels.index(key) # remember columns of requested data
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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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for output in options.output:
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if output == 'quaternion':
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table.labels_append(['%i_quaternion_%s'%(i+1,options.symmetry) for i in xrange(4)])
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if output == 'eulers':
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table.labels_append(['%i_eulers_%s'%(i+1,options.symmetry) for i in xrange(3)])
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# ------------------------------------------ assemble header ---------------------------------------
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table.head_write()
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# ------------------------------------------ process data ---------------------------------------
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while table.data_read(): # read next data line of ASCII table
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if input == 'eulers':
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o = damask.Orientation(Eulers=numpy.array(map(float,table.data[column['vector'][options.eulers]:\
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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=numpy.array([map(float,table.data[column['tensor'][options.matrix]:\
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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=numpy.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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)]).reshape(3,3),
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symmetry=options.symmetry).reduced()
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elif input == 'quaternion':
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o = damask.Orientation(quaternion=numpy.array(map(float,table.data[column['quaternion'][options.quaternion]:\
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column['quaternion'][options.quaternion]+datainfo['quaternion']['len']])),
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symmetry=options.symmetry).reduced()
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for output in options.output:
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if output == 'quaternion':
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table.data_append(o.asQuaternion())
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if output == 'eulers':
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table.data_append(o.asEulers('Bunge'))
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table.data_write() # output processed line
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# ------------------------------------------ output result ---------------------------------------
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table.output_flush() # just in case of buffered ASCII table
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if file['name'] != 'STDIN':
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file['input'].close() # close input ASCII table
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file['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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@ -48,6 +48,8 @@ bin_link = { \
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'addEuclideanDistance.py',
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'addMises.py',
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'addNorm.py',
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'addOrientations.py',
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'addIPFcolor.py',
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'addPK2.py',
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'addSchmidfactors.py',
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'addSpectralDecomposition.py',
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