failure in last commit, using standard keyword eulerangles instead of eulers
This commit is contained in:
Martin Diehl
parent
c2d27d56fa
commit
4e9b27b0ce
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#!/usr/bin/env python
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# -*- coding: UTF-8 no BOM -*-
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import os,sys,math,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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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('-c', '--configuration', dest='config', action='store_true',
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help='output material 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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#--- 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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'input':open(name),
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'output':open(name+'_tmp','w'),
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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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file['croak'].write('\033[1m' + scriptName + '\033[0m: ' + (file['name'] if file['name'] != 'STDIN' else '') + '\n')
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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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# --------------- read data -----------------------------------------------------------------------
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for line in file['input']:
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if line.strip():
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words = line.split()
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currPos = words[3:6]
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for i in xrange(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 xrange(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,words[:3])))
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phase.append(options.phase[int(float(words[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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file['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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file['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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for i,angle in enumerate(['phi1','PHI','phi2']):
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eulerangles[:,i]%=limits[i] # ensure, that rounded euler angles are not out of bounds (modulo by limits)
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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') # scale by desired precision and convert to int
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eulerKeys = np.array([int(''.join(map(formatString.format,euleranglesRadInt[i,:]))) \
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for i in xrange(info['grid'].prod())]) # create unique integer key from three euler angles by concatenating the string representation with leading zeros and store as integer
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devNull, texture, eulerKeys_idx = np.unique(eulerKeys, return_index = True, return_inverse=True)# search unique euler angle keys. Texture IDs are the indices of the first occurence, the inverse is used to construct the microstructure
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msFull = np.array([[eulerKeys_idx[i],phase[i]] for i in xrange(info['grid'].prod())],'i8') # create a microstructure (texture/phase pair) for each point using unique texture IDs. Use longInt (64bit, i8) because the keys might be long
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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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textureOut =['\n\n<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\n'
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for i in xrange(len(texture)):
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textureOut += ['[Texture%s]\n'%str(i+1).zfill(formatOut) +
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outStringAngles%tuple(eulerangles[texture[i],...])
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]
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formatOut = 1+int(math.log10(len(microstructure)))
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microstructureOut =['<microstructure>']
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for i in xrange(len(microstructure)):
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microstructureOut += ['[Grain%s]\n'%str(i+1).zfill(formatOut) +
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'crystallite\t%i\n'%options.crystallite +
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'(constituent)\tphase %i\ttexture %i\tfraction 1.0\n'%(microstructure[i,1],microstructure[i,0]+1)
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]
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info['microstructures'] = len(microstructure)
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#--- report ---------------------------------------------------------------------------------------
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file['croak'].write('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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file['croak'].write('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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file['croak'].write('invalid size x y z.\n')
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continue
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#--- write data -----------------------------------------------------------------------------------
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if options.config:
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file['output'].write('\n'.join(microstructureOut+ textureOut) + '\n')
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else:
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header = [' '.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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]
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file['output'].write('\n'.join(['%i\theader'%(len(header))] + header) + '\n')
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if options.compress:
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matPoints = matPoints.reshape([info['grid'][1]*info['grid'][2],info['grid'][0]])
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np.savetxt(file['output'],matPoints,fmt='%0'+str(1+int(math.log10(np.amax(matPoints))))+'d')
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else:
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file['output'].write("1 to %i\n"%(info['microstructures']))
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#--- output finalization --------------------------------------------------------------------------
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if file['name'] != 'STDIN':
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file['output'].close()
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os.rename(file['name']+'_tmp',
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os.path.splitext(file['name'])[0] +'%s'%('_material.config' if options.config else '.geom'))
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@ -0,0 +1,189 @@
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#!/usr/bin/env python
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# -*- coding: UTF-8 no BOM -*-
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import os,sys,math,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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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('-c', '--configuration', dest='config', action='store_true',
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help='output material 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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#--- 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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'input':open(name),
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'output':open(name+'_tmp','w'),
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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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file['croak'].write('\033[1m' + scriptName + '\033[0m: ' + (file['name'] if file['name'] != 'STDIN' else '') + '\n')
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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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# --------------- read data -----------------------------------------------------------------------
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for line in file['input']:
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if line.strip():
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words = line.split()
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currPos = words[3:6]
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for i in xrange(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 xrange(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,words[:3])))
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phase.append(options.phase[int(float(words[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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file['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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file['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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for i,angle in enumerate(['phi1','PHI','phi2']):
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eulerangles[:,i]%=limits[i] # ensure, that rounded euler angles are not out of bounds (modulo by limits)
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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') # scale by desired precision and convert to int
|
||||||
|
eulerKeys = np.array([int(''.join(map(formatString.format,euleranglesRadInt[i,:]))) \
|
||||||
|
for i in xrange(info['grid'].prod())]) # create unique integer key from three euler angles by concatenating the string representation with leading zeros and store as integer
|
||||||
|
devNull, texture, eulerKeys_idx = np.unique(eulerKeys, return_index = True, return_inverse=True)# search unique euler angle keys. Texture IDs are the indices of the first occurence, the inverse is used to construct the microstructure
|
||||||
|
msFull = np.array([[eulerKeys_idx[i],phase[i]] for i in xrange(info['grid'].prod())],'i8') # create a microstructure (texture/phase pair) for each point using unique texture IDs. Use longInt (64bit, i8) because the keys might be long
|
||||||
|
devNull,msUnique,matPoints = np.unique(msFull.view('c16'),True,True)
|
||||||
|
matPoints+=1
|
||||||
|
microstructure = np.array([msFull[i] for i in msUnique]) # pick only unique microstructures
|
||||||
|
else:
|
||||||
|
texture = np.arange(info['grid'].prod())
|
||||||
|
microstructure = np.hstack( zip(texture,phase) ).reshape(info['grid'].prod(),2) # create texture/phase pairs
|
||||||
|
formatOut = 1+int(math.log10(len(texture)))
|
||||||
|
textureOut =['\n\n<texture>']
|
||||||
|
|
||||||
|
eulerFormatOut='%%%i.%if'%(int(options.precision)+4,int(options.precision))
|
||||||
|
outStringAngles='(gauss) phi1 '+eulerFormatOut+' Phi '+eulerFormatOut+' phi2 '+eulerFormatOut+' scatter 0.0 fraction 1.0\n'
|
||||||
|
for i in xrange(len(texture)):
|
||||||
|
textureOut += ['[Texture%s]\n'%str(i+1).zfill(formatOut) +
|
||||||
|
outStringAngles%tuple(eulerangles[texture[i],...])
|
||||||
|
]
|
||||||
|
formatOut = 1+int(math.log10(len(microstructure)))
|
||||||
|
microstructureOut =['<microstructure>']
|
||||||
|
for i in xrange(len(microstructure)):
|
||||||
|
microstructureOut += ['[Grain%s]\n'%str(i+1).zfill(formatOut) +
|
||||||
|
'crystallite\t%i\n'%options.crystallite +
|
||||||
|
'(constituent)\tphase %i\ttexture %i\tfraction 1.0\n'%(microstructure[i,1],microstructure[i,0]+1)
|
||||||
|
]
|
||||||
|
|
||||||
|
info['microstructures'] = len(microstructure)
|
||||||
|
|
||||||
|
#--- report ---------------------------------------------------------------------------------------
|
||||||
|
file['croak'].write('grid a b c: %s\n'%(' x '.join(map(str,info['grid']))) +
|
||||||
|
'size x y z: %s\n'%(' x '.join(map(str,info['size']))) +
|
||||||
|
'origin x y z: %s\n'%(' : '.join(map(str,info['origin']))) +
|
||||||
|
'homogenization: %i\n'%info['homogenization'] +
|
||||||
|
'microstructures: %i\n\n'%info['microstructures'])
|
||||||
|
|
||||||
|
if np.any(info['grid'] < 1):
|
||||||
|
file['croak'].write('invalid grid a b c.\n')
|
||||||
|
continue
|
||||||
|
if np.any(info['size'] <= 0.0):
|
||||||
|
file['croak'].write('invalid size x y z.\n')
|
||||||
|
continue
|
||||||
|
|
||||||
|
|
||||||
|
#--- write data -----------------------------------------------------------------------------------
|
||||||
|
if options.config:
|
||||||
|
file['output'].write('\n'.join(microstructureOut+ textureOut) + '\n')
|
||||||
|
else:
|
||||||
|
header = [' '.join([scriptID] + sys.argv[1:]),
|
||||||
|
"grid\ta %i\tb %i\tc %i"%(info['grid'][0],info['grid'][1],info['grid'][2],),
|
||||||
|
"size\tx %f\ty %f\tz %f"%(info['size'][0],info['size'][1],info['size'][2],),
|
||||||
|
"origin\tx %f\ty %f\tz %f"%(info['origin'][0],info['origin'][1],info['origin'][2],),
|
||||||
|
"microstructures\t%i"%info['microstructures'],
|
||||||
|
"homogenization\t%i"%info['homogenization'],
|
||||||
|
]
|
||||||
|
file['output'].write('\n'.join(['%i\theader'%(len(header))] + header) + '\n')
|
||||||
|
if options.compress:
|
||||||
|
matPoints = matPoints.reshape([info['grid'][1]*info['grid'][2],info['grid'][0]])
|
||||||
|
np.savetxt(file['output'],matPoints,fmt='%0'+str(1+int(math.log10(np.amax(matPoints))))+'d')
|
||||||
|
else:
|
||||||
|
file['output'].write("1 to %i\n"%(info['microstructures']))
|
||||||
|
|
||||||
|
#--- output finalization --------------------------------------------------------------------------
|
||||||
|
if file['name'] != 'STDIN':
|
||||||
|
file['output'].close()
|
||||||
|
os.rename(file['name']+'_tmp',
|
||||||
|
os.path.splitext(file['name'])[0] +'%s'%('_material.config' if options.config else '.geom'))
|
||||||
|
|
||||||
|
|
@ -174,7 +174,7 @@ parser.set_defaults(grid = None,
|
||||||
position = 'pos',
|
position = 'pos',
|
||||||
weight = 'weight',
|
weight = 'weight',
|
||||||
microstructure = 'microstructure',
|
microstructure = 'microstructure',
|
||||||
eulers = 'Euler',
|
eulers = 'eulerangles',
|
||||||
homogenization = 1,
|
homogenization = 1,
|
||||||
crystallite = 1,
|
crystallite = 1,
|
||||||
phase = 1,
|
phase = 1,
|
||||||
|
|
|
||||||
Loading…
Reference in New Issue