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=addOrientation can do the same (and more)

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Martin Diehl 2016-03-09 19:02:28 +01:00
parent 63fe0c6b91
commit b0dedb8cbd
1 changed files with 0 additions and 100 deletions
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processing/post/addQuaternions.py
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#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
import os,sys,numpy as np
from optparse import OptionParser
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
Add Quaternions based on Crystal Frame Coordinates.
""", version = scriptID)
parser.add_option('-f','--frame',
dest='frame', nargs=4, type='string', metavar='<string string string string>',
help='heading of columns containing b* vector components and three frame vectors in that order')
parser.add_option('-s','--symmetry',
dest='crysym', nargs=1,type='string',metavar='<string>',
help='crystal symmetry definition')
parser.set_defaults(frame = None)
(options,filenames) = parser.parse_args()
if options.frame is None:
parser.error('no data column specified...')
datainfo = {'len':4,
'label':[]
}
if options.frame is not None: datainfo['label'] += options.frame
# --- loop over input files -------------------------------------------------------------------------
if filenames == []: filenames = [None]
for name in filenames:
try:
table = damask.ASCIItable(name = name,
buffered = False)
except: continue
damask.util.report(scriptName,name)
table.head_read() # read ASCII header info
# --------------- figure out columns to process ---------------------------------------------------
active = []
column = {}
for label in datainfo['label']:
key = '1_'+label if datainfo['len'] > 1 else label # non-special labels have to start with '1_'
if key in table.labels:
active.append(label)
column[label] = table.labels.index(key) # remember columns of requested data
else:
damask.util.croak('column %s not found...'%label)
# ------------------------------------------ assemble header ---------------------------------------
table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
table.labels_append(['Q_%i'%(i+1) for i in xrange(4)]) # extend ASCII header with new labels [1 real, 3 imaginary components]
table.head_write()
# ------------------------------------------ process data ------------------------------------------
outputAlive = True
while outputAlive and table.data_read(): # read next data line of ASCII table
vec = np.zeros([4,3])
for i,label in enumerate(active):
vec[i,:] = np.array(table.data[column[label]:
column[label]+3])
if sys.argv[1:][6]=='hexagonal': # Ensure Input matrix is orthogonal
M=np.dot(vec[0,:],vec[2,:])
vec[1,:]=vec[1,:]/np.linalg.norm(vec[1,:])
vec[2,:]=M*(vec[0,:]/np.linalg.norm(vec[0,:]))
vec[3,:]=vec[3,:]/np.linalg.norm(vec[3,:])
else:
vec[1,:]=vec[1,:]/np.linalg.norm(vec[1,:])
vec[2,:]=vec[2,:]/np.linalg.norm(vec[2,:])
vec[3,:]=vec[3,:]/np.linalg.norm(vec[3,:])
Ori=damask.Orientation(matrix=vec[1:,:],symmetry=sys.argv[1:][6])
table.data_append(np.asarray(Ori.asQuaternion()))
outputAlive = table.data_write() # output processed line
# ------------------------------------------ output result -----------------------------------------
outputAlive and table.output_flush() # just in case of buffered ASCII table
table.close() # close ASCII tables