Merge commit 'v2.0.2-1422-g00bcd7c3'
This commit is contained in:
Test User
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#!/usr/bin/env python2.7
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# -*- coding: UTF-8 no BOM -*-
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import os,sys,math
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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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scriptName = os.path.splitext(os.path.basename(__file__))[0]
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scriptID = ' '.join([scriptName,damask.version])
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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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Generate geometry description and material configuration from input files used by R.A. Lebensohn.
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""", version = scriptID)
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parser.add_option('--column', dest='column', type='int', metavar = 'int',
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help='data column to discriminate between both phases [%default]')
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parser.add_option('-t','--threshold', dest='threshold', type='float', metavar = 'float',
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help='threshold value for phase discrimination [%default]')
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parser.add_option('--homogenization', dest='homogenization', type='int', metavar = 'int',
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help='homogenization index for <microstructure> configuration [%default]')
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parser.add_option('--phase', dest='phase', type='int', nargs = 2, metavar = 'int int',
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help='phase indices for <microstructure> configuration %default')
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parser.add_option('--crystallite', dest='crystallite', type='int', metavar = 'int',
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help='crystallite index for <microstructure> configuration [%default]')
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parser.add_option('--compress', dest='compress', action='store_true',
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help='lump identical microstructure and texture information [%default]')
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parser.add_option('-p', '--precision', dest='precision', choices=['0','1','2','3'], metavar = 'int',
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help = 'euler angles decimal places for output format and compressing {0,1,2,3} [2]')
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parser.set_defaults(column = 7)
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parser.set_defaults(threshold = 1.0)
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parser.set_defaults(homogenization = 1)
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parser.set_defaults(phase = [1,2])
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parser.set_defaults(crystallite = 1)
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parser.set_defaults(config = False)
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parser.set_defaults(compress = False)
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parser.set_defaults(precision = '2')
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(options,filenames) = parser.parse_args()
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if filenames == []: filenames = [None]
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for name in filenames:
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try:
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table = damask.ASCIItable(name = name,
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outname = os.path.splitext(name)[-2]+'.geom' if name else name,
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buffered = False,
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labeled = False)
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except: continue
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damask.util.report(scriptName,name)
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info = {
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'grid': np.zeros(3,'i'),
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'size': np.zeros(3,'d'),
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'origin': np.zeros(3,'d'),
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'microstructures': 0,
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'homogenization': options.homogenization
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}
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coords = [{},{},{}]
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pos = {'min':[ float("inf"), float("inf"), float("inf")],
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'max':[-float("inf"),-float("inf"),-float("inf")]}
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phase = []
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eulerangles = []
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outputAlive = True
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# ------------------------------------------ process data ------------------------------------------
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while outputAlive and table.data_read():
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if table.data != []:
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currPos = table.data[3:6]
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for i in range(3):
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coords[i][currPos[i]] = True
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currPos = map(float,currPos)
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for i in range(3):
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pos['min'][i] = min(pos['min'][i],currPos[i])
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pos['max'][i] = max(pos['max'][i],currPos[i])
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eulerangles.append(map(math.degrees,map(float,table.data[:3])))
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phase.append(options.phase[int(float(table.data[options.column-1]) > options.threshold)])
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# --------------- determine size and grid ---------------------------------------------------------
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info['grid'] = np.array(map(len,coords),'i')
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info['size'] = info['grid']/np.maximum(np.ones(3,'d'),info['grid']-1.0)* \
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np.array([pos['max'][0]-pos['min'][0],
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pos['max'][1]-pos['min'][1],
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pos['max'][2]-pos['min'][2]],'d')
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eulerangles = np.array(eulerangles,dtype='f').reshape(info['grid'].prod(),3)
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phase = np.array(phase,dtype='i').reshape(info['grid'].prod())
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limits = [360,180,360]
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if any([np.any(eulerangles[:,i]>=limits[i]) for i in [0,1,2]]):
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damask.util.croak.write('Error: euler angles out of bound. Ang file might contain unidexed poins.\n')
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for i,angle in enumerate(['phi1','PHI','phi2']):
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for n in np.nditer(np.where(eulerangles[:,i]>=limits[i]),['zerosize_ok']):
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damask.util.croak.write('%s in line %i (%4.2f %4.2f %4.2f)\n'
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%(angle,n,eulerangles[n,0],eulerangles[n,1],eulerangles[n,2]))
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continue
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eulerangles=np.around(eulerangles,int(options.precision)) # round to desired precision
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# ensure, that rounded euler angles are not out of bounds (modulo by limits)
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for i,angle in enumerate(['phi1','PHI','phi2']):
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eulerangles[:,i]%=limits[i]
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# scale angles by desired precision and convert to int. create unique integer key from three euler angles by
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# concatenating the string representation with leading zeros and store as integer and search unique euler angle keys.
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# Texture IDs are the indices of the first occurrence, the inverse is used to construct the microstructure
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# create a microstructure (texture/phase pair) for each point using unique texture IDs.
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# Use longInt (64bit, i8) because the keys might be long
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if options.compress:
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formatString='{0:0>'+str(int(options.precision)+3)+'}'
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euleranglesRadInt = (eulerangles*10**int(options.precision)).astype('int')
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eulerKeys = np.array([int(''.join(map(formatString.format,euleranglesRadInt[i,:]))) \
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for i in range(info['grid'].prod())])
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devNull, texture, eulerKeys_idx = np.unique(eulerKeys, return_index = True, return_inverse=True)
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msFull = np.array([[eulerKeys_idx[i],phase[i]] for i in range(info['grid'].prod())],'i8')
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devNull,msUnique,matPoints = np.unique(msFull.view('c16'),True,True)
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matPoints+=1
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microstructure = np.array([msFull[i] for i in msUnique]) # pick only unique microstructures
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else:
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texture = np.arange(info['grid'].prod())
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microstructure = np.hstack( zip(texture,phase) ).reshape(info['grid'].prod(),2) # create texture/phase pairs
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formatOut = 1+int(math.log10(len(texture)))
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config_header = []
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formatwidth = 1+int(math.log10(len(microstructure)))
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config_header += ['<microstructure>']
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for i in range(len(microstructure)):
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config_header += ['[Grain%s]'%str(i+1).zfill(formatwidth),
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'crystallite\t%i'%options.crystallite,
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'(constituent)\tphase %i\ttexture %i\tfraction 1.0'%(microstructure[i,1],microstructure[i,0]+1)
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]
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config_header += ['<texture>']
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eulerFormatOut='%%%i.%if'%(int(options.precision)+4,int(options.precision))
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outStringAngles='(gauss) phi1 '+eulerFormatOut+' Phi '+eulerFormatOut+' phi2 '+eulerFormatOut+' scatter 0.0 fraction 1.0'
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for i in range(len(texture)):
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config_header += ['[Texture%s]'%str(i+1).zfill(formatOut),
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outStringAngles%tuple(eulerangles[texture[i],...])
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]
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table.labels_clear()
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table.info_clear()
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info['microstructures'] = len(microstructure)
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#--- report ---------------------------------------------------------------------------------------
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damask.util.croak('grid a b c: %s\n'%(' x '.join(map(str,info['grid']))) +
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'size x y z: %s\n'%(' x '.join(map(str,info['size']))) +
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'origin x y z: %s\n'%(' : '.join(map(str,info['origin']))) +
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'homogenization: %i\n'%info['homogenization'] +
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'microstructures: %i\n\n'%info['microstructures'])
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if np.any(info['grid'] < 1):
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damask.util.croak('invalid grid a b c.\n')
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continue
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if np.any(info['size'] <= 0.0):
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damask.util.croak('invalid size x y z.\n')
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continue
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#--- write data -----------------------------------------------------------------------------------
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table.info_append([' '.join([scriptID] + sys.argv[1:]),
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"grid\ta %i\tb %i\tc %i"%(info['grid'][0],info['grid'][1],info['grid'][2],),
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"size\tx %f\ty %f\tz %f"%(info['size'][0],info['size'][1],info['size'][2],),
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"origin\tx %f\ty %f\tz %f"%(info['origin'][0],info['origin'][1],info['origin'][2],),
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"microstructures\t%i"%info['microstructures'],
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"homogenization\t%i"%info['homogenization'],
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config_header
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])
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table.head_write()
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if options.compress:
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table.data = matPoints.reshape(info['grid'][1]*info['grid'][2],info['grid'][0])
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table.data_writeArray('%%%ii'%(formatwidth),delimiter=' ')
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else:
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table.data = ["1 to %i\n"%(info['microstructures'])]
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# ------------------------------------------ output finalization -----------------------------------
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table.close()
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