215 lines
11 KiB
Python
Executable File
215 lines
11 KiB
Python
Executable File
#!/usr/bin/env python
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# -*- coding: UTF-8 no BOM -*-
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import os,sys,math,string,numpy as np
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from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
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scriptID = '$Id$'
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scriptName = scriptID.split()[1]
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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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#--------------------------------------------------------------------------------------------------
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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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Generate geometry description and material configuration from EBSD data in given square-gridded 'ang' file.
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Two phases can be discriminated based on threshold value in a given data column.
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""" + string.replace(scriptID,'\n','\\n')
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)
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parser.add_option('--column', dest='column', type='int', metavar = 'int', \
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help='data column to discriminate phase 1 from 2 [%default]')
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parser.add_option('-t','--threshold', dest='threshold', type='float', metavar = 'float', \
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help='threshold value to discriminate phase 1 from 2 [%default]')
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parser.add_option('--homogenization', dest='homogenization', type='int', metavar = 'int', \
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help='homogenization index to be used [%default]')
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parser.add_option('--phase', dest='phase', type='int', nargs = 2, metavar = 'int int', \
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help='two phase indices to be used %default')
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parser.add_option('--crystallite', dest='crystallite', type='int', metavar = 'int', \
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help='crystallite index to be used [%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='search for matching mircrostructure and texture and lump them [%default]')
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parser.add_option('-a', '--axes', dest='axes', type='string', nargs = 3, metavar = 'string string string', \
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help='axes assignement of eulerangles x,y,z = %default')
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parser.set_defaults(column = 11)
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parser.set_defaults(threshold = 0.5)
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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(axes = ['y','x','-z'])
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(options,filenames) = parser.parse_args()
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for i in options.axes:
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if i.lower() not in ['x','+x','-x','y','+y','-y','z','+z','-z']:
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file['croak'].write('invalid axes %s %s %s' %(options.axes[0],options.axes[1],options.axes[2]))
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sys.exit()
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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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if file['name'] != 'STDIN': file['croak'].write('\033[1m'+scriptName+'\033[0m: '+file['name']+'\n')
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else: file['croak'].write('\033[1m'+scriptName+'\033[0m\n')
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info = {
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'grid': np.ones (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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step = [0,0]
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point = 0
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for line in file['input']:
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words = line.split()
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if words[0] == '#': # process initial comments block
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if len(words) > 2:
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if words[2].lower() == 'hexgrid':
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file['croak'].write('The file has HexGrid format. Please first convert to SquareGrid...\n')
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sys.exit()
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if words[1] == 'XSTEP:': step[0] = float(words[2])
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if words[1] == 'YSTEP:': step[1] = float(words[2])
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if words[1] == 'NCOLS_ODD:':
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info['grid'][0] = int(words[2])
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eulerangles = np.zeros((info['grid'][0]*info['grid'][1],3),dtype='f')
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phase = np.zeros(info['grid'][0]*info['grid'][1],dtype='i')
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if words[1] == 'NROWS:':
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info['grid'][1] = int(words[2])
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eulerangles = np.zeros((info['grid'][0]*info['grid'][1],3),dtype='f')
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phase = np.zeros(info['grid'][0]*info['grid'][1],dtype='i')
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else: # finished with comments block
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phase[point] = options.phase[{True:0,False:1}[float(words[options.column-1])<options.threshold]]
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eulerangles[point,...] = map(lambda x: float(x)*180.0/math.pi, words[:3])
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point += 1
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if info['grid'].prod() != point:
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file['croak'].write('Error: found %s microstructures. Header info in ang file might be wrong.\n'%point)
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sys.exit()
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if options.compress:
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texture = []
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microstructure = []
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otherPoint=-1 # ensure to create first microstructure
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matPoints = np.zeros(info['grid'][0]*info['grid'][1],dtype='i')
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for myPoint in xrange(info['grid'][0]*info['grid'][1]):
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myTexture=-1
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for otherPoint in xrange(len(microstructure)):
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otherEulers = eulerangles[texture[microstructure[otherPoint][0]]]
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otherPhase = phase[[microstructure[otherPoint][1]]]
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if all(eulerangles[myPoint]==otherEulers) and phase[myPoint] == otherPhase: # common microstructure
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matPoints[myPoint] = otherPoint+1 # use other points microstructure
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otherPoint =-4 # in no case, create new microstructure
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break
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elif all(eulerangles[myPoint]==otherEulers): # found common texture and store it
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myTexture = microstructure[otherPoint][0]
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if otherPoint == len(microstructure)-1 or otherPoint == -2: #
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if myTexture == -1:
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texture.append(myPoint)
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myTexture = len(texture)-1
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microstructure.append([myTexture,myPoint])
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matPoints[myPoint] = len(microstructure) # use the new microstructure
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else:
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texture = [i for i in xrange(info['grid'][0]*info['grid'][1])]
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microstructure = [[i+1,phase[i]] for i in xrange(info['grid'][0]*info['grid'][1])]
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matPoints = np.arange(info['grid'][0]*info['grid'][1],dtype='i')
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formatOut = 1+int(math.log10(len(texture)))
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textureOut =['\n\n<texture>']
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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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'axes %s %s %s\n'%(options.axes[0],options.axes[1],options.axes[2]) +\
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'(gauss)\tphi1 %4.2f\tPhi %4.2f\tphi2 %4.2f\tscatter 0.0\tfraction 1.0\n'%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 %s\tfraction 1.0\n'%(phase[microstructure[i][1]],microstructure[i][0]+1)
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]
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info['microstructures'] = len(microstructure)
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info['size'] = step[0]*info['grid'][0],step[1]*info['grid'][1],min(step)
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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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sys.exit()
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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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sys.exit()
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#--- write data -----------------------------------------------------------------------------------
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if options.config:
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file['output'].write('\n'.join(microstructureOut) + \
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'\n'.join(textureOut))
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else:
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header = [scriptID + ' ' + ' '.join(sys.argv[1:]) + '\n']
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header.append("grid\ta %i\tb %i\tc %i\n"%(info['grid'][0],info['grid'][1],info['grid'][2],))
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header.append("size\tx %f\ty %f\tz %f\n"%(info['size'][0],info['size'][1],info['size'][2],))
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header.append("origin\tx %f\ty %f\tz %f\n"%(info['origin'][0],info['origin'][1],info['origin'][2],))
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header.append("microstructures\t%i\n"%info['microstructures'])
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header.append("homogenization\t%i\n"%info['homogenization'])
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file['output'].write('%i\theader\n'%(len(header))+''.join(header))
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if options.compress:
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matPoints = matPoints.reshape((info['grid'][1],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',os.path.splitext(file['name'])[0] + \
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{True: '_material.config',
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False:'.geom'}[options.config])
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