Add x,y coordinates of stereographic projection of given direction (pole) in crystal frame.
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Philip Eisenlohr
parent
05d7adaf25
commit
89f8ba979e
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#!/usr/bin/env python
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# -*- coding: UTF-8 no BOM -*-
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import os,sys,string
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import numpy as np
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from optparse import OptionParser
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import damask
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scriptID = string.replace('$Id$','\n','\\n')
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scriptName = os.path.splitext(scriptID.split()[1])[0]
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# --------------------------------------------------------------------
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# MAIN
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# --------------------------------------------------------------------
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parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
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Add x,y coordinates of stereographic projection of given direction (pole) in crystal frame.
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""", version = scriptID)
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parser.add_option('-p', '--pole', dest='pole', type='float', nargs=3, metavar='float float float',
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help = 'crystal frame direction for pole figure %default')
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parser.add_option('--polar', dest='polar', action='store_true',
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help = 'output polar coordinates r,phi [%default]')
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parser.add_option('-e', '--eulers', dest='eulers', 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', metavar='string',
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help = 'orientation matrix label')
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parser.add_option('-a', dest='a', metavar='string',
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help = 'crystal frame a vector label')
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parser.add_option('-b', dest='b', metavar='string',
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help = 'crystal frame b vector label')
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parser.add_option('-c', dest='c', metavar='string',
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help = 'crystal frame c vector label')
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parser.add_option('-q', '--quaternion', dest='quaternion', metavar='string',
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help = 'quaternion label')
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parser.set_defaults(pole = [1.0,0.0,0.0])
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parser.set_defaults(degrees = False)
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parser.set_defaults(polar = 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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'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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input = []
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if options.eulers != None:
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datainfo['vector']['label'] += [options.eulers]
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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:
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datainfo['vector']['label'] += [options.a,options.b,options.c]
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input += ['frame']
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if options.matrix != None:
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datainfo['tensor']['label'] += [options.matrix]
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input += ['matrix']
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if options.quaternion != None:
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datainfo['quaternion']['label'] += [options.quaternion]
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input += ['quaternion']
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if len(input) != 1: parser.error('needs exactly one input format...')
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input = input[0]
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toRadians = np.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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files = []
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if filenames == []:
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files.append({'name':'STDIN',
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'input':sys.stdin,
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'output':sys.stdout,
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'croak':sys.stderr,
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})
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else:
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for name in filenames:
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if os.path.exists(name):
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files.append({'name':name,
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'croak':sys.stdout,
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})
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#--- loop over input files ------------------------------------------------------------------------
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for file in files:
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if file['name'] != 'STDIN':
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file['input'] = open(file['name'])
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file['output'] = open(file['name']+'_tmp','w')
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file['croak'].write('\033[1m' + scriptName + '\033[0m' + (': '+file['name'] if file['name'] != 'STDIN' else '') + '\n')
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table = damask.ASCIItable(file['input'],file['output'],buffered = False) # make unbuffered ASCII_table
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table.head_read() # read ASCII header info
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table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
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column = {}
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missingColumns = False
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for datatype,info in datainfo.items():
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for label in info['label']:
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key = list(set([label, '1_'+label]) & set(table.labels))
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if key == []:
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file['croak'].write('column %s not found...\n'%label)
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missingColumns = True # break if label not found
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else:
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column[label] = table.labels.index(key[0]) # remember columns of requested data
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if missingColumns:
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continue
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# ------------------------------------------ assemble header ---------------------------------------
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table.labels_append(['%i_pole_%g%g%g'%(i+1,options.pole[0],options.pole[1],options.pole[2]) for i in xrange(2)])
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table.head_write()
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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*\
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np.array(map(float,table.data[column[options.eulers]:\
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column[options.eulers]+datainfo['vector']['len']])),
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)
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elif input == 'matrix':
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o = damask.Orientation(matrix=\
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np.array([map(float,table.data[column[options.matrix]:\
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column[options.matrix]+datainfo['tensor']['len']])]).reshape(np.sqrt(datainfo['tensor']['len']),
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np.sqrt(datainfo['tensor']['len'])).transpose(),
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)
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elif input == 'frame':
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o = damask.Orientation(matrix=\
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np.array([map(float,table.data[column[options.a]:\
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column[options.a]+datainfo['vector']['len']] + \
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table.data[column[options.b]:\
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column[options.b]+datainfo['vector']['len']] + \
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table.data[column[options.c]:\
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column[options.c]+datainfo['vector']['len']]
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)]).reshape(3,3),
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)
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elif input == 'quaternion':
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o = damask.Orientation(quaternion=\
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np.array(map(float,table.data[column[options.quaternion]:\
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column[options.quaternion]+datainfo['quaternion']['len']])),
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)
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rotatedPole = o.quaternion*pole # rotate pole according to crystal orientation
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(x,y) = rotatedPole[0:2]/(1.+abs(pole[2])) # stereographic projection
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table.data_append([np.sqrt(x*x+y*y),np.arctan2(y,x)] if options.polar else [x,y]) # cartesian coordinates
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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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table.input_close() # close input ASCII table (works for stdin)
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table.output_close() # close output ASCII table (works for stdout)
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if file['name'] != 'STDIN':
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os.rename(file['name']+'_tmp',file['name']) # overwrite old one with tmp new
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