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some more changes improving the post processing scripts

This commit is contained in:
Martin Diehl 2014-07-22 14:21:49 +00:00
parent 1707f7d367
commit e5dc9e79cc
8 changed files with 111 additions and 141 deletions
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10
processing/post/3Dvisualize.py
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@ -274,7 +274,7 @@ parser.add_option('-v', '--vector', action='extend', dest='vector', type='string
help='list of vectors to visualize', metavar = '<string LIST>') help='list of vectors to visualize', metavar = '<string LIST>')
parser.add_option('-t', '--tensor', action='extend', dest='tensor', type='string', \ parser.add_option('-t', '--tensor', action='extend', dest='tensor', type='string', \
help='list of tensors to visualize', metavar = '<string LIST>') help='list of tensors to visualize', metavar = '<string LIST>')
parser.add_option('-d', '--deformation', dest='defgrad', type='string', \ parser.add_option('-d', '--deformation', dest='defgrad', action='store', type='string', \
help='heading of deformation gradient columns [%default]', metavar = 'string') help='heading of deformation gradient columns [%default]', metavar = 'string')
parser.add_option('--reference', dest='undeformed', action='store_true',\ parser.add_option('--reference', dest='undeformed', action='store_true',\
help='map results to reference (undeformed) configuration [%default]') help='map results to reference (undeformed) configuration [%default]')
@ -290,15 +290,15 @@ parser.add_option('--points', dest='output_points', action='store_true', \
help='produce VTK points file [%default]') help='produce VTK points file [%default]')
parser.add_option('--nopoints', dest='output_points', action='store_false', \ parser.add_option('--nopoints', dest='output_points', action='store_false', \
help='omit VTK points file') help='omit VTK points file')
parser.add_option('--separator', dest='separator', type='string', \ parser.add_option('--separator', dest='separator', action='store', type='string', \
help='data separator (t(ab), n(ewline), s(pace)) [%default]', metavar = 'string') help='data separator (t(ab), n(ewline), s(pace)) [%default]', metavar = 'string')
parser.add_option('--scaling', dest='scaling', action='extend', type='string', \ parser.add_option('--scaling', dest='scaling', action='extend', type='string', \
help='scaling of fluctuation', metavar = '<float LIST>') help='scaling of fluctuation', metavar = '<float LIST>')
parser.add_option('-u', '--unitlength', dest='unitlength', type='float', \ parser.add_option('-u', '--unitlength', dest='unitlength', action='store', type='float', \
help='set unit length for 2D model [%default]', metavar = 'float') help='set unit length for 2D model [%default]', metavar = 'float')
parser.add_option('--filenodalcoords', dest='filenodalcoords', type='string', \ parser.add_option('--filenodalcoords', dest='filenodalcoords', action='store', type='string', \
help='ASCII table containing nodal coords', metavar = 'string') help='ASCII table containing nodal coords', metavar = 'string')
parser.add_option('--labelnodalcoords', dest='labelnodalcoords', type='string', nargs=3, \ parser.add_option('--labelnodalcoords', dest='labelnodalcoords', action='store', type='string', nargs=3, \
help='labels of nodal coords in ASCII table %default', metavar = 'string string string') help='labels of nodal coords in ASCII table %default', metavar = 'string string string')
parser.add_option('-l', '--linear', dest='linearreconstruction', action='store_true',\ parser.add_option('-l', '--linear', dest='linearreconstruction', action='store_true',\
help='use linear reconstruction of geometry [%default]') help='use linear reconstruction of geometry [%default]')

4
processing/post/addCauchy.py
View File

@ -21,9 +21,9 @@ deformation gradient and first Piola--Kirchhoff stress.
""", version = string.replace(scriptID,'\n','\\n') """, version = string.replace(scriptID,'\n','\\n')
) )
parser.add_option('-f','--defgrad', dest='defgrad', type='string', metavar='string', \ parser.add_option('-f','--defgrad', dest='defgrad', action='store', type='string', metavar='string', \
help='heading of columns containing deformation gradient [%default]') help='heading of columns containing deformation gradient [%default]')
parser.add_option('-p','--stress', dest='stress', type='string', metavar='string', \ parser.add_option('-p','--stress', dest='stress', action='store', type='string', metavar='string', \
help='heading of columns containing first Piola--Kirchhoff stress [%default]') help='heading of columns containing first Piola--Kirchhoff stress [%default]')
parser.set_defaults(defgrad = 'f') parser.set_defaults(defgrad = 'f')
parser.set_defaults(stress = 'p') parser.set_defaults(stress = 'p')

4
processing/post/addCompatibilityMismatch.py
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@ -24,9 +24,9 @@ parser.add_option('--no-shape','-s', dest='noShape', action='store_false', \
help='do not calcuate shape mismatch [%default]') help='do not calcuate shape mismatch [%default]')
parser.add_option('--no-volume','-v', dest='noVolume', action='store_false', \ parser.add_option('--no-volume','-v', dest='noVolume', action='store_false', \
help='do not calculate volume mismatch [%default]') help='do not calculate volume mismatch [%default]')
parser.add_option('-c','--coordinates', dest='coords', type='string', metavar='string', \ parser.add_option('-c','--coordinates', dest='coords', action='store', type='string', metavar='string', \
help='column heading for coordinates [%default]') help='column heading for coordinates [%default]')
parser.add_option('-f','--deformation', dest='defgrad', type='string', metavar='string ', \ parser.add_option('-f','--deformation', dest='defgrad', action='store', type='string', metavar='string ', \
help='column heading for coordinates [%defgrad]') help='column heading for coordinates [%defgrad]')
parser.set_defaults(noVolume = False) parser.set_defaults(noVolume = False)
parser.set_defaults(noShape = False) parser.set_defaults(noShape = False)

2
processing/post/addCurl.py
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@ -22,7 +22,7 @@ Deals with both vector- and tensor-valued fields.
""", version = string.replace(scriptID,'\n','\\n') """, version = string.replace(scriptID,'\n','\\n')
) )
parser.add_option('-c','--coordinates', dest='coords', type='string', metavar='string', \ parser.add_option('-c','--coordinates', dest='coords', action='store', type='string', metavar='string', \
help='column heading for coordinates [%default]') help='column heading for coordinates [%default]')
parser.add_option('-v','--vector', dest='vector', action='extend', type='string', metavar='<string LIST>', \ parser.add_option('-v','--vector', dest='vector', action='extend', type='string', metavar='<string LIST>', \
help='heading of columns containing vector field values') help='heading of columns containing vector field values')

4
processing/post/addDeformedConfiguration.py
View File

@ -21,9 +21,9 @@ Operates on periodic ordered three-dimensional data sets.
""", version = string.replace(scriptID,'\n','\\n') """, version = string.replace(scriptID,'\n','\\n')
) )
parser.add_option('-c','--coordinates', dest='coords', type='string', metavar='string', \ parser.add_option('-c','--coordinates', dest='coords', action='store', type='string', metavar='string', \
help='column heading for coordinates [%default]') help='column heading for coordinates [%default]')
parser.add_option('-d','--defgrad', dest='defgrad', type='string', metavar='string', \ parser.add_option('-d','--defgrad', dest='defgrad', action='store', type='string', metavar='string', \
help='heading of columns containing tensor field values') help='heading of columns containing tensor field values')
parser.add_option('-l', '--linear', dest='linearreconstruction', action='store_true',\ parser.add_option('-l', '--linear', dest='linearreconstruction', action='store_true',\
help='use linear reconstruction of geometry [%default]') help='use linear reconstruction of geometry [%default]')

2
processing/post/addDivergence.py
View File

@ -27,7 +27,7 @@ parser.add_option('--fdm', dest='accuracy', action='extend', type='
help='degree of central difference accuracy (%s)'%(','.join(accuracyChoices))) help='degree of central difference accuracy (%s)'%(','.join(accuracyChoices)))
parser.add_option('--fft', dest='fft', action='store_true', \ parser.add_option('--fft', dest='fft', action='store_true', \
help='calculate divergence in Fourier space') help='calculate divergence in Fourier space')
parser.add_option('-c','--coordinates', dest='coords', type='string', metavar = 'string', \ parser.add_option('-c','--coordinates', dest='coords', action='store', type='string', metavar = 'string', \
help='column heading for coordinates [%default]') help='column heading for coordinates [%default]')
parser.add_option('-v','--vector', dest='vector', action='extend', type='string', metavar='<string LIST>', \ parser.add_option('-v','--vector', dest='vector', action='extend', type='string', metavar='<string LIST>', \
help='heading of columns containing vector field values') help='heading of columns containing vector field values')

135
processing/post/addEuclideanDistance.py
View File

@ -1,39 +1,25 @@
#!/usr/bin/env python #!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*- # -*- coding: UTF-8 no BOM -*-
import os,re,sys,math,numpy,string,damask import os,re,sys,math,string
import numpy as np
from optparse import OptionParser
from scipy import ndimage from scipy import ndimage
from optparse import OptionParser, Option import damask
# -----------------------------
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)
scriptID = '$Id$'
scriptName = scriptID.split()[1]
def periodic_3Dpad(array, rimdim=(1,1,1)): def periodic_3Dpad(array, rimdim=(1,1,1)):
rimdim = numpy.array(rimdim,'i') rimdim = np.array(rimdim,'i')
size = numpy.array(array.shape,'i') size = np.array(array.shape,'i')
padded = numpy.empty(size+2*rimdim,array.dtype) padded = np.empty(size+2*rimdim,array.dtype)
padded[rimdim[0]:rimdim[0]+size[0], padded[rimdim[0]:rimdim[0]+size[0],
rimdim[1]:rimdim[1]+size[1], rimdim[1]:rimdim[1]+size[1],
rimdim[2]:rimdim[2]+size[2]] = array rimdim[2]:rimdim[2]+size[2]] = array
p = numpy.zeros(3,'i') p = np.zeros(3,'i')
for side in xrange(3): for side in xrange(3):
for p[(side+2)%3] in xrange(padded.shape[(side+2)%3]): for p[(side+2)%3] in xrange(padded.shape[(side+2)%3]):
for p[(side+1)%3] in xrange(padded.shape[(side+1)%3]): for p[(side+1)%3] in xrange(padded.shape[(side+1)%3]):
@ -56,7 +42,7 @@ features = [ \
] ]
neighborhoods = { neighborhoods = {
'neumann':numpy.array([ 'neumann':np.array([
[-1, 0, 0], [-1, 0, 0],
[ 1, 0, 0], [ 1, 0, 0],
[ 0,-1, 0], [ 0,-1, 0],
@ -64,7 +50,7 @@ neighborhoods = {
[ 0, 0,-1], [ 0, 0,-1],
[ 0, 0, 1], [ 0, 0, 1],
]), ]),
'moore':numpy.array([ 'moore':np.array([
[-1,-1,-1], [-1,-1,-1],
[ 0,-1,-1], [ 0,-1,-1],
[ 1,-1,-1], [ 1,-1,-1],
@ -95,22 +81,22 @@ neighborhoods = {
]) ])
} }
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 Euclidean distance to grain structural features: Add column(s) containing Euclidean distance to grain structural features:
boundaries, triple lines, and quadruple points. boundaries, triple lines, and quadruple points.
""" + string.replace('$Id$','\n','\\n') """, version = string.replace(scriptID,'\n','\\n')
) )
parser.add_option('-i','--identifier', dest='id', action='store', type='string', \ parser.add_option('-c','--coordinates', dest='coords', action='store', type='string', metavar='string', \
help='heading of column containing grain identifier [%default]', \ help='column heading for coordinates [%default]')
metavar='<label>') parser.add_option('-i','--identifier', dest='id', action='store', type='string', metavar = 'string', \
parser.add_option('-t','--type', dest='type', action='extend', type='string', \ help='heading of column containing grain identifier [%default]')
parser.add_option('-t','--type', dest='type', action='extend', type='string', metavar='<string LIST>', \
help='feature type (%s)'%(', '.join(map(lambda x:', '.join(x['names']),features)))) help='feature type (%s)'%(', '.join(map(lambda x:', '.join(x['names']),features))))
parser.add_option('-n','--neighborhood', dest='neigborhood', action='store', type='string', \ parser.add_option('-n','--neighborhood',dest='neigborhood', action='store', type='string', metavar='int', \
help='type of neighborhood (%s)'%(', '.join(neighborhoods.keys())), \ help='type of neighborhood (%s)'%(', '.join(neighborhoods.keys())))
metavar='<int>') parser.set_defaults(coords = 'ip')
parser.set_defaults(type = []) parser.set_defaults(type = [])
parser.set_defaults(id = 'texture') parser.set_defaults(id = 'texture')
parser.set_defaults(neighborhood = 'neumann') parser.set_defaults(neighborhood = 'neumann')
@ -126,60 +112,61 @@ for i,feature in enumerate(features):
for name in feature['names']: for name in feature['names']:
for type in options.type: for type in options.type:
if name.startswith(type): if name.startswith(type):
feature_list.append(i) # remember valid features feature_list.append(i) # remember valid features
break break
# ------------------------------------------ setup file handles --------------------------------------- # ------------------------------------------ setup file handles -----------------------------------
files = [] files = []
if filenames == []: for name in filenames:
files.append({'name':'STDIN', 'input':sys.stdin, 'output':sys.stdout, 'croak':sys.stderr}) if os.path.exists(name):
else: files.append({'name':name, 'input':open(name), 'output':open(name+'_tmp','w'), 'croak':sys.stderr})
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 ---------------------------------------
# ------------------------------------------ loop over input files ---------------------------------
for file in files: for file in files:
if file['name'] != 'STDIN': file['croak'].write(file['name']+'\n') file['croak'].write('\033[1m'+scriptName+'\033[0m: '+file['name']+'\n')
table = damask.ASCIItable(file['input'],file['output'],False) # make unbuffered ASCII_table table = damask.ASCIItable(file['input'],file['output'],False) # make unbuffered ASCII_table
table.head_read() # read ASCII header info table.head_read() # read ASCII header info
table.info_append(string.replace('$Id$','\n','\\n') + \ table.info_append(string.replace(scriptID,'\n','\\n') + '\t' + ' '.join(sys.argv[1:]))
'\t' + ' '.join(sys.argv[1:]))
# ------------------------------------------ assemble header --------------------------------------- # --------------- figure out position of labels and coordinates ------------------------------------
try:
locationCol = table.labels.index('%s.x'%options.coords) # columns containing location data
except ValueError:
file['croak'].write('no coordinate data found...\n'%key)
continue
if options.id not in table.labels: if options.id not in table.labels:
file['croak'].write('column %s not found...\n'%options.id) file['croak'].write('column %s not found...\n'%options.id)
continue continue
# ------------------------------------------ assemble header ---------------------------------------
for feature in feature_list: for feature in feature_list:
table.labels_append('ED_%s(%s)'%(features[feature]['names'][0],options.id)) # extend ASCII header with new labels table.labels_append('ED_%s(%s)'%(features[feature]['names'][0],options.id)) # extend ASCII header with new labels
table.head_write() table.head_write()
# ------------------------------------------ process data --------------------------------------- # ------------------------------------------ process data ---------------------------------------
table.data_readArray(['ip.x','ip.y','ip.z',options.id]) table.data_readArray([options.coords+'.x',options.coords+'.y',options.coords+'.z',options.id])
grid = [{},{},{}] grid = [{},{},{}]
for i in xrange(len(table.data)): for i in xrange(len(table.data)):
for j in xrange(3): for j in xrange(3):
grid[j][str(table.data[i,j])] = True grid[j][str(table.data[i,j])] = True
resolution = numpy.array(map(len,grid),'i') resolution = np.array(map(len,grid),'i')
unitlength = 0.0 unitlength = 0.0
for i,r in enumerate(resolution): for i,r in enumerate(resolution):
if r > 1: unitlength = max(unitlength,(max(map(float,grid[i].keys()))-min(map(float,grid[i].keys())))/(r-1.0)) if r > 1: unitlength = max(unitlength,(max(map(float,grid[i].keys()))-min(map(float,grid[i].keys())))/(r-1.0))
neighborhood = neighborhoods[options.neighborhood] neighborhood = neighborhoods[options.neighborhood]
convoluted = numpy.empty([len(neighborhood)]+list(resolution+2),'i') convoluted = np.empty([len(neighborhood)]+list(resolution+2),'i')
microstructure = periodic_3Dpad(numpy.array(table.data[:,3].reshape(resolution),'i')) microstructure = periodic_3Dpad(np.array(table.data[:,3].reshape(resolution),'i'))
for i,p in enumerate(neighborhood): for i,p in enumerate(neighborhood):
stencil = numpy.zeros((3,3,3),'i') stencil = np.zeros((3,3,3),'i')
stencil[1,1,1] = -1 stencil[1,1,1] = -1
stencil[p[0]+1, stencil[p[0]+1,
p[1]+1, p[1]+1,
@ -187,36 +174,34 @@ for file in files:
convoluted[i,:,:,:] = ndimage.convolve(microstructure,stencil) convoluted[i,:,:,:] = ndimage.convolve(microstructure,stencil)
distance = numpy.ones((len(feature_list),resolution[0],resolution[1],resolution[2]),'d') distance = np.ones((len(feature_list),resolution[0],resolution[1],resolution[2]),'d')
convoluted = numpy.sort(convoluted,axis=0) convoluted = np.sort(convoluted,axis=0)
uniques = numpy.zeros(resolution) uniques = np.zeros(resolution)
check = numpy.empty(resolution) check = np.empty(resolution)
check[:,:,:] = numpy.nan check[:,:,:] = np.nan
for i in xrange(len(neighborhood)): for i in xrange(len(neighborhood)):
uniques += numpy.where(convoluted[i,1:-1,1:-1,1:-1] == check,0,1) uniques += np.where(convoluted[i,1:-1,1:-1,1:-1] == check,0,1)
check = convoluted[i,1:-1,1:-1,1:-1] check = convoluted[i,1:-1,1:-1,1:-1]
for i,feature_id in enumerate(feature_list): for i,feature_id in enumerate(feature_list):
distance[i,:,:,:] = numpy.where(uniques > features[feature_id]['aliens'],0.0,1.0) distance[i,:,:,:] = np.where(uniques > features[feature_id]['aliens'],0.0,1.0)
for i in xrange(len(feature_list)): for i in xrange(len(feature_list)):
distance[i,:,:,:] = ndimage.morphology.distance_transform_edt(distance[i,:,:,:])*[unitlength]*3 distance[i,:,:,:] = ndimage.morphology.distance_transform_edt(distance[i,:,:,:])*[unitlength]*3
distance.shape = (len(feature_list),resolution.prod()) distance.shape = (len(feature_list),resolution.prod())
# ------------------------------------------ process data ---------------------------------------
table.data_rewind() table.data_rewind()
l = 0 l = 0
while table.data_read(): while table.data_read():
for i in xrange(len(feature_list)): for i in xrange(len(feature_list)):
table.data_append(distance[i,l]) # add all distance fields table.data_append(distance[i,l]) # add all distance fields
table.data_write() # output processed line outputAlive = table.data_write() # output processed line
l += 1 l += 1
# ------------------------------------------ output result --------------------------------------- # ------------------------------------------ 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': os.rename(file['name']+'_tmp',file['name']) # overwrite old one with tmp new
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

91
processing/post/addIPFcolor.py
View File

@ -1,56 +1,43 @@
#!/usr/bin/env python #!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*- # -*- coding: UTF-8 no BOM -*-
import os,sys,string,re,math,numpy import os,re,sys,math,string
import damask import numpy as np
from collections import defaultdict from collections import defaultdict
from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP from optparse import OptionParser
import damask
scriptID = '$Id$' scriptID = '$Id$'
scriptName = scriptID.split()[1] scriptName = scriptID.split()[1]
#-------------------------------------------------------------------------------------------------- # --------------------------------------------------------------------
class extendedOption(Option): # MAIN
#-------------------------------------------------------------------------------------------------- # --------------------------------------------------------------------
# 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): parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
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 RGB color value corresponding to TSL-OIM scheme for inverse pole figures. Add RGB color value corresponding to TSL-OIM scheme for inverse pole figures.
""" + string.replace(scriptID,'\n','\\n')
""", version = string.replace(scriptID,'\n','\\n')
) )
parser.add_option('-p', '--pole', dest='pole', type='float', nargs=3, metavar='X Y Z', parser.add_option('-p', '--pole', dest='pole', type='float', nargs=3, metavar='X Y Z',
help = 'lab frame direction for inverse pole figure %default') help = 'lab frame direction for inverse pole figure %default')
parser.add_option('-s', '--symmetry', dest='symmetry', type='string', parser.add_option('-s', '--symmetry', dest='symmetry', type='string',
help = 'crystal symmetry [%default]') help = 'crystal symmetry [%default]')
parser.add_option('-e', '--eulers', dest='eulers', type='string', metavar='LABEL', parser.add_option('-e', '--eulers', dest='eulers', type='string', metavar='LABEL',
help = 'Euler angles label') help = 'Euler angles label')
parser.add_option('-d', '--degrees', dest='degrees', action='store_true', parser.add_option('-d', '--degrees', dest='degrees', action='store_true',
help = 'Euler angles are given in degrees [%default]') help = 'Euler angles are given in degrees [%default]')
parser.add_option('-m', '--matrix', dest='matrix', type='string', metavar='LABEL', parser.add_option('-m', '--matrix', dest='matrix', type='string', metavar='LABEL',
help = 'orientation matrix label') help = 'orientation matrix label')
parser.add_option('-a', dest='a', type='string', metavar='LABEL', parser.add_option('-a', dest='a', type='string', metavar='LABEL',
help = 'crystal frame a vector label') help = 'crystal frame a vector label')
parser.add_option('-b', dest='b', type='string', metavar='LABEL', parser.add_option('-b', dest='b', type='string', metavar='LABEL',
help = 'crystal frame b vector label') help = 'crystal frame b vector label')
parser.add_option('-c', dest='c', type='string', metavar='LABEL', parser.add_option('-c', dest='c', type='string', metavar='LABEL',
help = 'crystal frame c vector label') help = 'crystal frame c vector label')
parser.add_option('-q', '--quaternion', dest='quaternion', type='string', metavar='LABEL', parser.add_option('-q', '--quaternion', dest='quaternion', type='string', metavar='LABEL',
help = 'quaternion label') help = 'quaternion label')
parser.set_defaults(pole = [0.0,0.0,1.0]) parser.set_defaults(pole = [0.0,0.0,1.0])
parser.set_defaults(symmetry = 'cubic') parser.set_defaults(symmetry = 'cubic')
@ -75,8 +62,8 @@ if options.matrix != None: datainfo['tensor']['label'] += [options.matrix];
if options.quaternion != None: datainfo['quaternion']['label'] += [options.quaternion]; input = 'quaternion' 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 toRadians = math.pi/180.0 if options.degrees else 1.0 # rescale degrees to radians
pole = numpy.array(options.pole) pole = np.array(options.pole)
pole /= numpy.linalg.norm(pole) pole /= np.linalg.norm(pole)
# ------------------------------------------ setup file handles --------------------------------------- # ------------------------------------------ setup file handles ---------------------------------------
@ -124,15 +111,15 @@ for file in files:
while table.data_read(): # read next data line of ASCII table while table.data_read(): # read next data line of ASCII table
if input == 'eulers': if input == 'eulers':
o = damask.Orientation(Eulers=toRadians*numpy.array(map(float,table.data[column['vector'][options.eulers]:\ o = damask.Orientation(Eulers=toRadians*np.array(map(float,table.data[column['vector'][options.eulers]:\
column['vector'][options.eulers]+datainfo['vector']['len']])), column['vector'][options.eulers]+datainfo['vector']['len']])),
symmetry=options.symmetry).reduced() symmetry=options.symmetry).reduced()
elif input == 'matrix': elif input == 'matrix':
o = damask.Orientation(matrix=numpy.array([map(float,table.data[column['tensor'][options.matrix]:\ o = damask.Orientation(matrix=np.array([map(float,table.data[column['tensor'][options.matrix]:\
column['tensor'][options.matrix]+datainfo['tensor']['len']])]), column['tensor'][options.matrix]+datainfo['tensor']['len']])]),
symmetry=options.symmetry).reduced() symmetry=options.symmetry).reduced()
elif input == 'frame': elif input == 'frame':
o = damask.Orientation(matrix=numpy.array([map(float,table.data[column['vector'][options.a]:\ o = damask.Orientation(matrix=np.array([map(float,table.data[column['vector'][options.a]:\
column['vector'][options.a]+datainfo['vector']['len']] + \ column['vector'][options.a]+datainfo['vector']['len']] + \
table.data[column['vector'][options.b]:\ table.data[column['vector'][options.b]:\
column['vector'][options.b]+datainfo['vector']['len']] + \ column['vector'][options.b]+datainfo['vector']['len']] + \
@ -141,19 +128,17 @@ for file in files:
)]).reshape(3,3), )]).reshape(3,3),
symmetry=options.symmetry).reduced() symmetry=options.symmetry).reduced()
elif input == 'quaternion': elif input == 'quaternion':
o = damask.Orientation(quaternion=numpy.array(map(float,table.data[column['quaternion'][options.quaternion]:\ o = damask.Orientation(quaternion=np.array(map(float,table.data[column['quaternion'][options.quaternion]:\
column['quaternion'][options.quaternion]+datainfo['quaternion']['len']])), column['quaternion'][options.quaternion]+datainfo['quaternion']['len']])),
symmetry=options.symmetry).reduced() symmetry=options.symmetry).reduced()
table.data_append(o.IPFcolor(pole)) table.data_append(o.IPFcolor(pole))
outputAlive = table.data_write() # output processed line
table.data_write() # output processed line
# ------------------------------------------ output result --------------------------------------- # ------------------------------------------ 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': if file['name'] != 'STDIN':
file['input'].close() # close input ASCII table os.rename(file['name']+'_tmp',file['name']) # overwrite old one with tmp new
file['output'].close() # close output ASCII table
os.rename(file['name']+'_tmp',file['name']) # overwrite old one with tmp new