improved search for double microstructures (was N^2 bogosort) in geom_fromAng and introduced it in geom_fromVPSC
This commit is contained in:
Martin Diehl
parent
b08141d2b3
commit
e01e270300
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@ -19,23 +19,24 @@ Two phases can be discriminated based on threshold value in a given data column.
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""", version = scriptID)
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parser.add_option('--column', dest='column', type='int', metavar = 'int', \
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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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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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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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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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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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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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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('-a', '--axes', dest='axes', nargs = 3, metavar = 'string string string', \
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parser.add_option('-a', '--axes', dest='axes', nargs = 3, metavar = 'string string string',
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help='Euler angle coordinate system for <texture> configuration x,y,z = %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 = 11)
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parser.set_defaults(threshold = 0.5)
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@ -45,8 +46,10 @@ 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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parser.set_defaults(precision = '2')
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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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parser.error('invalid axes %s %s %s' %(options.axes[0],options.axes[1],options.axes[2]))
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@ -68,7 +71,6 @@ else:
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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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@ -86,78 +88,70 @@ for file in files:
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for line in file['input']:
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words = line.split()
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if len(words) == 0: continue # ignore empty lines
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if words[0] == '#': # process initial comments block
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if words[0] == '#': # process initial comments/header 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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break
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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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if words[1] == 'NCOLS_ODD:': # ignore order of NROWS/NCOLS
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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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eulerangles = np.empty((info['grid'].prod(),3),dtype='f')
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phase = np.empty(info['grid'].prod(),dtype='i')
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if words[1] == 'NROWS:': # ignore order of NROWS/NCOLS
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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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eulerangles = np.empty((info['grid'].prod(),3),dtype='f')
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phase = np.empty(info['grid'].prod(),dtype='i')
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else: # finished with comments block
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phase[point] = options.phase[int(float(words[options.column-1]) > options.threshold)]
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eulerangles[point,...] = map(lambda x: math.degrees(float(x)), 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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continue
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if np.any(np.max(eulerangles[0,:])>=360) or np.any(np.max(eulerangles[1,:])>=180) or np.any(np.max(eulerangles[2,:])>=360):
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file['croak'].write('Error: euler angles out of bound. Ang file might contain unidexed poins.\n')
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#continue
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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'].prod(),dtype='i') # index of microstructure in geom file
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for myPoint in xrange(info['grid'].prod()):
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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 = microstructure[otherPoint][1]
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if all(abs(eulerangles[myPoint]-otherEulers)<1e-6) and phase[myPoint] == otherPhase: # common microstructure
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matPoints[myPoint] = otherPoint+1 # use other point's microstructure, +1 because starting with 1 (.config) instead of 0 (python)
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otherPoint = -2 # never 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: # did not found matching microstructure
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if myTexture == -1: # did not even found matching texture
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myTexture = len(texture)
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texture.append(myPoint)
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microstructure.append([myTexture,phase[myPoint]])
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matPoints[myPoint] = len(microstructure) # use the new microstructure
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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 = [i for i in xrange(info['grid'][0]*info['grid'][1])]
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microstructure = [[i,phase[i]] for i in xrange(info['grid'][0]*info['grid'][1])]
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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(texture[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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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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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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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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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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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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@ -13,22 +13,26 @@ scriptName = os.path.splitext(scriptID.split()[1])[0]
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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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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 phase 1 from 2 [%default]')
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parser.add_option('-t','--treshold', 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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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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@ -36,6 +40,8 @@ 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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@ -69,62 +75,93 @@ for file in files:
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'homogenization': options.homogenization
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}
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needInfo = [True,True,True]
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microstructure = ['<microstructure>']
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texture = ['<texture>']
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phase = []
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eulerangles = []
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point = 0
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for line in file['input']:
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if line.strip():
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point += 1
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words = line.split()
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currPos = map(float,words[3:6])
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for i in xrange(3):
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if currPos[i] > info['grid'][i]:
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info['size'][i] = currPos[i]
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info['grid'][i]+=1
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if options.config: # write configuration (line by line)
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me = str(point)
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microstructure += ['[Grain%s]\n'%me + \
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'crystallite\t%i\n'%options.crystallite + \
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'(constituent)\tphase %s\ttexture %s\tfraction 1.0\n'%(options.phase[{True:0,False:1}[float(words[options.column-1])<options.threshold]],me)
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eulerangles.append(map(float,words[:3]))
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phase.append(options.phase[int(float(words[options.column-1]) > options.threshold)])
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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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if np.any(np.max(eulerangles[0,:])>=360) or np.any(np.max(eulerangles[1,:])>=180) or np.any(np.max(eulerangles[2,:])>=360):
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file['croak'].write('Error: euler angles out of bounds.\n')
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continue
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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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texture += ['[Grain%s]\n'%me + \
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'(gauss)\tphi1 %s\tPhi %s\tphi2 %s\tscatter 0.0\tfraction 1.0\n'%tuple(words[:3])
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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'] = info['grid'][0]*info['grid'][1]*info['grid'][2]
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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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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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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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sys.exit()
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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(microstructure) + \
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'\n'.join(texture))
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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'][0]))
|
||||
np.savetxt(file['output'],matPoints,fmt='%0'+str(1+int(math.log10(np.amax(matPoints))))+'d')
|
||||
else:
|
||||
header = [scriptID + ' ' + ' '.join(sys.argv[1:])+'\n']
|
||||
header.append("grid\ta %i\tb %i\tc %i\n"%(info['grid'][0],info['grid'][1],info['grid'][2],))
|
||||
header.append("size\tx %f\ty %f\tz %f\n"%(info['size'][0],info['size'][1],info['size'][2],))
|
||||
header.append("origin\tx %f\ty %f\tz %f\n"%(info['origin'][0],info['origin'][1],info['origin'][2],))
|
||||
header.append("microstructures\t%i\n"%info['microstructures'])
|
||||
header.append("homogenization\t%i\n"%info['homogenization'])
|
||||
file['output'].write('%i\theader\n'%(len(header))+''.join(header))
|
||||
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] + \
|
||||
{True: '_material.config',
|
||||
False:'.geom'}[options.config])
|
||||
os.rename(file['name']+'_tmp',
|
||||
os.path.splitext(file['name'])[0] +'%s'%('_material.config' if options.config else '.geom'))
|
||||
|
|
|
|||
Loading…
Reference in New Issue