#!/usr/bin/env python # -*- coding: UTF-8 no BOM -*- import os,sys,string,itertools,re,math,numpy import damask from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP 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",) 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 = """\ 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') ) parser.add_option('-o', '--orientations', dest='output', action='append', metavar='', help = 'output orientation formats') parser.add_option('-s', '--symmetry', dest='symmetry', type='string', help = 'crystal symmetry [%default]') 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 = 'Euler 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') parser.set_defaults(output = []) parser.set_defaults(symmetry = 'cubic') parser.set_defaults(degrees = False) (options, filenames) = parser.parse_args() datainfo = { # list of requested labels per datatype 'tensor': {'len':9, 'label':[]}, 'vector': {'len':3, 'label':[]}, 'quaternion': {'len':4, 'label':[]}, } if options.eulers != None: datainfo['vector']['label'] += [options.eulers]; input = 'eulers' if options.a != None and \ options.b != None and \ options.c != None: datainfo['vector']['label'] += [options.a,options.b,options.c]; input = 'frame' if options.matrix != None: datainfo['tensor']['label'] += [options.matrix]; input = 'matrix' if options.quaternion != None: datainfo['quaternion']['label'] += [options.quaternion]; input = 'quaternion' toRadians = math.pi/180.0 if options.degrees else 1.0 # rescale degrees to radians options.output = map(lambda x: x.lower(), options.output) # ------------------------------------------ setup file handles --------------------------------------- files = [] if filenames == []: 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'), 'croak':sys.stderr}) #--- 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.info_append(string.replace(scriptID,'\n','\\n') + '\t' + ' '.join(sys.argv[1:])) # --------------- figure out columns to process active = {} column = {} head = [] 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 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 if not foundIt: file['croak'].write('column %s not found...\n'%label) break 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 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']])), symmetry=options.symmetry).reduced() elif input == 'matrix': o = damask.Orientation(matrix=numpy.array([map(float,table.data[column['tensor'][options.matrix]:\ column['tensor'][options.matrix]+datainfo['tensor']['len']])]), symmetry=options.symmetry).reduced() elif input == 'frame': o = damask.Orientation(matrix=numpy.array([map(float,table.data[column['vector'][options.a]:\ column['vector'][options.a]+datainfo['vector']['len']] + \ table.data[column['vector'][options.b]:\ column['vector'][options.b]+datainfo['vector']['len']] + \ table.data[column['vector'][options.c]:\ column['vector'][options.c]+datainfo['vector']['len']] )]).reshape(3,3), symmetry=options.symmetry).reduced() elif input == 'quaternion': o = damask.Orientation(quaternion=numpy.array(map(float,table.data[column['quaternion'][options.quaternion]:\ column['quaternion'][options.quaternion]+datainfo['quaternion']['len']])), symmetry=options.symmetry).reduced() for output in options.output: if output == 'quaternion': table.data_append(o.asQuaternion()) if output == 'eulers': table.data_append(o.asEulers('Bunge')) table.data_write() # output processed line # ------------------------------------------ output result --------------------------------------- table.output_flush() # just in case of buffered ASCII table 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