renamed spectral_buildElements.py to nodesFromCentroids.py and added first simple version of an ascii table to ang converter
This commit is contained in:
Martin Diehl
parent
299d9e6bc4
commit
b7dc9f9944
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@ -344,6 +344,10 @@ parser.add_option('--scaling', dest='scaling', type='float', \
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help='scaling of fluctuation [%default]')
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parser.add_option('-u', '--unitlength', dest='unitlength', type='float', \
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help='set unit length for 2D model [%default]')
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parser.add_option('--filenodalcoords', dest='filenodalcoords', type='string', \
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help='ASCII table containing nodal coords')
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parser.add_option('--labelnodalcoords', dest='nodalcoords', type='string', \
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help='labels of nodal coords in ASCII table')
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parser.add_option('-l', '--linear', dest='linearreconstruction', action='store_true',\
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help='use linear reconstruction of geometry [%default]')
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@ -362,12 +366,15 @@ parser.set_defaults(scaling = 1.0)
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parser.set_defaults(undeformed = False)
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parser.set_defaults(unitlength = 0.0)
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parser.set_defaults(cell = True)
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parser.set_defaults(filenodalcoords = '')
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parser.set_defaults(labelnodalcoords = 'coord')
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parser.set_defaults(linearreconstruction = False)
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sep = {'n': '\n', 't': '\t', 's': ' '}
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(options, args) = parser.parse_args()
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if options.scaling !=1.0 and options.linearreconstruction: print 'cannot scale for linear reconstruction'
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if options.scaling !=1.0 and options.filenodalcoords!='': print 'cannot scale when reading coordinate from file'
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options.separator = options.separator.lower()
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for filename in args:
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if not os.path.exists(filename):
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@ -453,23 +460,34 @@ for filename in args:
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else:
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dim[2] = options.unitlength
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if options.filenodalcoords:
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mesh = numpy.zeros(((res[0]+1)*(res[1]+1)*(res[2]+1),3),'d')
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mesh=mesh.reshape(res[0]+1,res[1]+1,res[2]+1,3)
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filenodalcoords = open(options.filenodalcoords)
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tablenodalcoords = damask.ASCIItable(filenodalcoords)
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tablenodalcoords.head_read()
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coord = tablenodalcoords.labels.index(options.labelnodalcoords+'.x')
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i = 0
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while tablenodalcoords.data_read():
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mesh[i%(res[0]+1),(i//(res[0]+1))%(res[1]+1),(i//(res[0]+1)//(res[1]+1)) % (res[2]+1),:]=\
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[float(tablenodalcoords.data[coord]),
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float(tablenodalcoords.data[coord+1]),
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float(tablenodalcoords.data[coord+2])]
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i += 1
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else:
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F = numpy.reshape(values[:,column['tensor'][options.defgrad]: column['tensor'][options.defgrad]+9],(res[0],res[1],res[2],3,3))
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if options.undeformed:
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defgrad_av = numpy.eye(3)
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Favg = numpy.eye(3)
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else:
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defgrad_av = damask.core.math.tensorAvg(numpy.reshape(values[:,column['tensor'][options.defgrad]:
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column['tensor'][options.defgrad]+9],
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(res[0],res[1],res[2],3,3)))
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Favg = damask.core.math.tensorAvg(F)
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if options.linearreconstruction:
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centroids = damask.core.mesh.deformed_linear(res,dim,defgrad_av,
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numpy.reshape(values[:,column['tensor'][options.defgrad]:
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column['tensor'][options.defgrad]+9],
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(res[0],res[1],res[2],3,3)))
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centroids = damask.core.mesh.deformed_linear(res,dim,Favg,F)
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else:
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centroids = damask.core.mesh.deformed_fft(res,dim,defgrad_av,options.scaling,
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numpy.reshape(values[:,column['tensor'][options.defgrad]:
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column['tensor'][options.defgrad]+9],
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(res[0],res[1],res[2],3,3)))
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ms = damask.core.mesh.mesh_regular_grid(res,dim,defgrad_av,centroids)
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centroids = damask.core.mesh.deformed_fft(res,dim,Favg,options.scaling,F)
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mesh = damask.core.mesh.mesh_regular_grid(res,dim,Favg,centroids)
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fields = {\
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'tensor': {},\
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'vector': {},\
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@ -505,9 +523,9 @@ for filename in args:
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print '\n'
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out = {}
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if options.output_mesh: out['mesh'] = vtk_writeASCII_mesh(ms,fields,res,sep[options.separator])
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if options.output_mesh: out['mesh'] = vtk_writeASCII_mesh(mesh,fields,res,sep[options.separator])
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if options.output_points: out['points'] = vtk_writeASCII_points(centroids,fields,res,sep[options.separator])
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if options.output_box: out['box'] = vtk_writeASCII_box(dim,defgrad_av)
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if options.output_box: out['box'] = vtk_writeASCII_box(dim,Favg)
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for what in out.keys():
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print what
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@ -48,9 +48,12 @@ parser.add_option('-c','--coordinates', dest='coords', type='string',\
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help='column heading for coordinates [%default]')
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parser.add_option('-d','--defgrad', dest='defgrad', type='string', \
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help='heading of columns containing tensor field values')
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parser.add_option('-l', '--linear', dest='linearreconstruction', action='store_true',\
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help='use linear reconstruction of geometry [%default]')
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parser.set_defaults(coords = 'ip')
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parser.set_defaults(defgrad = 'f' )
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parser.set_defaults(linearreconstruction = False)
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(options,filenames) = parser.parse_args()
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@ -115,7 +118,7 @@ for file in files:
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sys.stderr.write('column %s not found...\n'%key)
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else:
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defgrad = numpy.array([0.0 for i in xrange(N*9)]).reshape(list(res)+[3,3])
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table.labels_append(['%s_deformed'%(coord) for coord in 'x','y','z']) # extend ASCII header with new labels
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table.labels_append(['ip_deformed.%s'%(coord) for coord in 'x','y','z']) # extend ASCII header with new labels
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column = table.labels.index(key)
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# ------------------------------------------ assemble header ---------------------------------------
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@ -134,8 +137,10 @@ for file in files:
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# ------------------------------------------ process value field ----------------------------
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defgrad_av = damask.core.math.tensorAvg(defgrad)
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if options.linearreconstruction:
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centroids = damask.core.mesh.deformed_fft(res,geomdim,defgrad_av,1.0,defgrad)
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else:
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centroids = damask.core.mesh.deformed_fft(res,geomdim,defgrad_av,1.0,defgrad)
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# ------------------------------------------ process data ---------------------------------------
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table.data_rewind()
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@ -38,17 +38,20 @@ def index(location,res):
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# --------------------------------------------------------------------
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parser = OptionParser(option_class=extendableOption, usage='%prog options [file[s]]', description = """
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Calculates current coordinates and nodal displacement from IP/FP based deformation gradient.
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Calculates current nodal coordinates and nodal displacement from IP/FP based data.
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""" + string.replace('$Id$','\n','\\n')
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)
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parser.add_option('-c','--coordinates', dest='coords', type='string',\
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help='column heading for coordinates [%default]')
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parser.add_option('-d','--defgrad', dest='defgrad', type='string', \
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help='heading of columns containing tensor field values')
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parser.add_option('-d','--deformed', dest='deformedCentroids', type='string',\
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help='column heading for position of deformed center of element/IP [%default]')
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parser.add_option('-u','--undeformed', dest='undeformedCentroids', type='string',\
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help='column heading for position of undeformed center of element/IP [%default]')
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parser.add_option('-f','--defgrad', dest='defgrad', type='string',\
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help='column heading for position of deformation gradient [%default]')
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parser.set_defaults(coords = 'ip')
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parser.set_defaults(deformedCentroids = 'ip_deformed')
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parser.set_defaults(undeformedCentroids = 'ip')
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parser.set_defaults(defgrad = 'f')
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(options,filenames) = parser.parse_args()
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@ -75,7 +78,7 @@ for file in files:
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# --------------- figure out dimension and resolution
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try:
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locationCol = table.labels.index('%s.x'%options.coords) # columns containing location data
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locationCol = table.labels.index('%s.x'%options.undeformedCentroids) # columns containing location data
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except ValueError:
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print 'no coordinate data found...'
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continue
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@ -108,37 +111,49 @@ for file in files:
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# --------------- figure out columns to process
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key = '%s.x' %options.deformedCentroids
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if key not in table.labels:
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sys.stderr.write('column %s not found...\n'%key)
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else:
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columnDeformed = table.labels.index(key)
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key = '%s.x' %options.undeformedCentroids
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if key not in table.labels:
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sys.stderr.write('column %s not found...\n'%key)
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else:
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columnUndeformed = table.labels.index(key)
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key = '1_%s' %options.defgrad
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if key not in table.labels:
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sys.stderr.write('column %s not found...\n'%key)
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else:
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column = table.labels.index(key)
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columnDefgrad = table.labels.index(key)
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# ------------------------------------------ read value field ---------------------------------------
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deformedCentroids = numpy.array([0.0 for i in xrange(N*3)]).reshape(list(res)+[3])
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undeformedCentroids = numpy.array([0.0 for i in xrange(N*3)]).reshape(list(res)+[3])
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defgrad = numpy.array([0.0 for i in xrange(N*9)]).reshape(list(res)+[3,3])
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table.data_rewind()
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table.data_read()
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inc = table.data[table.labels.index('inc')]
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inc = int(eval(table.data[table.labels.index('inc')]))
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table.data_rewind()
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idx = 0
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while table.data_read(): # read next data line of ASCII table
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(x,y,z) = location(idx,res) # figure out (x,y,z) position from line count
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idx += 1
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defgrad[x,y,z] = numpy.array(map(float,table.data[column:column+9]),'d').reshape(3,3)
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deformedCentroids[x,y,z] = numpy.array(map(float,table.data[columnDeformed:columnDeformed+3]),'d')
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undeformedCentroids[x,y,z] = numpy.array(map(float,table.data[columnUndeformed:columnUndeformed+3]),'d')
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defgrad[x,y,z] = numpy.array(map(float,table.data[columnDefgrad:columnDefgrad+9]),'d').reshape(3,3)
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file['input'].close() # close input ASCII table
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# ------------------------------------------ process value field ----------------------------
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defgrad_av = damask.core.math.tensorAvg(defgrad)
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centroids = damask.core.mesh.deformed_fft(res,geomdim,defgrad_av,1.0,defgrad)
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nodes = damask.core.mesh.mesh_regular_grid(res,geomdim,defgrad_av,centroids)
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defgrad_av = damask.core.math.math_tensorAvg(defgrad)
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nodesDeformed = damask.core.mesh.mesh_regular_grid(res,geomdim,defgrad_av,deformedCentroids)
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nodesUndeformed = damask.core.mesh.mesh_regular_grid(res,geomdim,numpy.identity(3,'d'),undeformedCentroids)
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# ------------------------------------------ process data ---------------------------------------
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@ -156,7 +171,7 @@ for file in files:
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for y in xrange(res[1]+1):
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for x in xrange(res[0]+1):
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ielem +=1
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entry = [inc,0,ielem,0,0,'\t'.join([str(a) for a in(nodes[x][y][z])]),'\t'.join([str(a) for a in (nodes[x][y][z] - (x,y,z)*(geomdim/res))])]
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entry = [inc,0,ielem,0,0,'\t'.join([str(a) for a in(nodesUndeformed[x][y][z])]),'\t'.join([str(a) for a in (nodesUndeformed[x][y][z] - nodesDeformed[x][y][z])])]
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table.data_append(entry)
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table.data_write() # output processed line
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table.data_clear()
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@ -0,0 +1,194 @@
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#!/usr/bin/env python
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import os,re,sys,math,string,damask,numpy
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from optparse import OptionParser, Option
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# -----------------------------
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class extendableOption(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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def integerFactorization(i):
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j = int(math.floor(math.sqrt(float(i))))
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while (j>1 and int(i)%j != 0):
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j -= 1
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return j
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def positiveRadians(angle):
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angle = math.radians(float(angle))
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while angle < 0.0:
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angle += 2.0*math.pi
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return angle
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def getHeader(sizeX,sizeY,step):
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return [ \
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'# TEM_PIXperUM 1.000000', \
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'# x-star 0.509548', \
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'# y-star 0.795272', \
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'# z-star 0.611799', \
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'# WorkingDistance 18.000000', \
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'#', \
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'# Phase 1', \
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'# MaterialName Al', \
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'# Formula Fe', \
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'# Info', \
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'# Symmetry 43', \
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'# LatticeConstants 2.870 2.870 2.870 90.000 90.000 90.000', \
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'# NumberFamilies 4', \
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'# hklFamilies 1 1 0 1 0.000000 1', \
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'# hklFamilies 2 0 0 1 0.000000 1', \
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'# hklFamilies 2 1 1 1 0.000000 1', \
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'# hklFamilies 3 1 0 1 0.000000 1', \
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'# Categories 0 0 0 0 0 ', \
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'#', \
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'# GRID: SquareGrid', \
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'# XSTEP: ' + str(step), \
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'# YSTEP: ' + str(step), \
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'# NCOLS_ODD: ' + str(sizeX), \
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'# NCOLS_EVEN: ' + str(sizeX), \
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'# NROWS: ' + str(sizeY), \
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'#', \
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'# OPERATOR: ODFsammpling', \
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'#', \
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'# SAMPLEID: ', \
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'#', \
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'# SCANID: ', \
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'#', \
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]
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# --------------------------------------------------------------------
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# MAIN
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# --------------------------------------------------------------------
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parser = OptionParser(option_class=extendableOption, usage='%prog options [file[s]]', description = """
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Builds an ang file out of ASCII table.
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""" + string.replace('$Id$','\n','\\n')
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)
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parser.add_option('--coords', dest='coords', type='string', \
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help='label of coords in ASCII table')
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parser.set_defaults(norm = 'ip')
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(options,filenames) = parser.parse_args()
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datainfo = {
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'vector': {'len':3,
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'label':[]}
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}
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datainfo['vector']['label'] += ['eulerangles']
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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})
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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)})
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# ------------------------------------------ loop over input files ---------------------------------------
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for file in files:
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if file['name'] != 'STDIN': print file['name']
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table = damask.ASCIItable(file['input']) # open ASCII_table for reading
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table.head_read() # read ASCII header info
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# --------------- figure out dimension and resolution
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try:
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locationCol = table.labels.index('ip.x') # columns containing location data
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except ValueError:
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print 'no coordinate data found...'
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continue
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grid = [{},{},{}]
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while table.data_read(): # read next data line of ASCII table
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for j in xrange(3):
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grid[j][str(table.data[locationCol+j])] = True # remember coordinate along x,y,z
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resolution = numpy.array([len(grid[0]),\
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len(grid[1]),\
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len(grid[2]),],'i') # resolution is number of distinct coordinates found
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dimension = resolution/numpy.maximum(numpy.ones(3,'d'),resolution-1.0)* \
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numpy.array([max(map(float,grid[0].keys()))-min(map(float,grid[0].keys())),\
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max(map(float,grid[1].keys()))-min(map(float,grid[1].keys())),\
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max(map(float,grid[2].keys()))-min(map(float,grid[2].keys())),\
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],'d') # dimension from bounding box, corrected for cell-centeredness
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if resolution[2] == 1:
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dimension[2] = min(dimension[:2]/resolution[:2])
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N = resolution.prod()
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print '\t%s @ %s'%(dimension,resolution)
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# --------------- figure out columns to process
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active = {}
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column = {}
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values = {}
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divergence = {}
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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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key = {True :'1_%s',
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False:'%s' }[info['len']>1]%label
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if key not in table.labels:
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sys.stderr.write('column %s not found...\n'%key)
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else:
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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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if datatype not in values: values[datatype] = {}
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if datatype not in divergence: divergence[datatype] = {}
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if label not in divergence[datatype]: divergence[datatype][label] = {}
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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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values[datatype][label] = numpy.array([0.0 for i in xrange(N*datainfo[datatype]['len'])])
|
||||
|
||||
# ------------------------------------------ read value field ---------------------------------------
|
||||
|
||||
table.data_rewind()
|
||||
print values['vector']['eulerangles']
|
||||
print numpy.shape(values['vector']['eulerangles'])
|
||||
idx = 0
|
||||
while table.data_read(): # read next data line of ASCII table
|
||||
for datatype,labels in active.items(): # loop over vector,tensor
|
||||
for label in labels: # loop over all requested curls
|
||||
values[datatype][label][idx:idx+3]= numpy.array(map(float,table.data[column[datatype][label]:
|
||||
column[datatype][label]+datainfo[datatype]['len']]),'d')
|
||||
idx+=3
|
||||
for z in xrange(resolution[2]):
|
||||
fileOut=open(os.path.join(os.path.dirname(name),os.path.splitext(os.path.basename(name))[0]+'_%s.ang'%z),'w')
|
||||
for line in getHeader(resolution[0],resolution[1],1.0):
|
||||
fileOut.write(line + '\n')
|
||||
|
||||
# write data
|
||||
for counter in xrange(resolution[0]*resolution[1]):
|
||||
print z*resolution[0]*resolution[1]*3+counter*3,' - ',z*resolution[0]*resolution[1]*3+counter*3+3
|
||||
fileOut.write(''.join(['%10.5f'%positiveRadians(angle) for angle in values['vector']['eulerangles'][z*resolution[0]*resolution[1]*3+counter*3:z*resolution[0]*resolution[1]*3+counter*3+3]])+
|
||||
''.join(['%10.5f'%coord for coord in [counter%resolution[0],counter//resolution[1]]])+
|
||||
' 100.0 1.0 0 1 1.0\n')
|
||||
counter += 1
|
||||
|
||||
fileOut.close()
|
||||
|
||||
|
|
@ -116,8 +116,9 @@ bin_link = { \
|
|||
'postResults.py',
|
||||
'spectral_iterationCount.py',
|
||||
'spectral_parseLog.py',
|
||||
'spectral_buildElements.py',
|
||||
'nodesFromCentroids.py',
|
||||
'tagLabel.py',
|
||||
'table2ang',
|
||||
],
|
||||
}
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue