modernized string formatting, updated help strings, using label_indexrange for data-slicing.
This commit is contained in:
Philip Eisenlohr
parent
45e237058b
commit
9e5a8d2391
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@ -112,84 +112,92 @@ Generate geometry description and material configuration by standard Voronoi tes
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group = OptionGroup(parser, "Tessellation","")
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group.add_option('-l', '--laguerre',
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dest = 'laguerre',
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action = 'store_true',
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help = 'use Laguerre (weighted Voronoi) tessellation')
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group.add_option('-l',
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'--laguerre',
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dest = 'laguerre',
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action = 'store_true',
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help = 'use Laguerre (weighted Voronoi) tessellation')
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group.add_option('--cpus',
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dest = 'cpus',
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type = 'int', metavar = 'int',
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help = 'number of parallel processes to use for Laguerre tessellation [%default]')
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dest = 'cpus',
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type = 'int', metavar = 'int',
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help = 'number of parallel processes to use for Laguerre tessellation [%default]')
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group.add_option('--nonperiodic',
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dest = 'nonperiodic',
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action = 'store_true',
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help = 'use nonperiodic tessellation')
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dest = 'nonperiodic',
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action = 'store_true',
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help = 'nonperiodic tessellation')
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parser.add_option_group(group)
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group = OptionGroup(parser, "Geometry","")
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group.add_option('-g', '--grid',
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dest = 'grid',
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type = 'int', nargs = 3, metavar = ' '.join(['int']*3),
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help = 'a,b,c grid of hexahedral box [auto]')
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group.add_option('-s', '--size',
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dest = 'size',
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type = 'float', nargs = 3, metavar=' '.join(['float']*3),
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help = 'x,y,z size of hexahedral box [auto]')
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group.add_option('-o', '--origin',
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dest = 'origin',
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type = 'float', nargs = 3, metavar=' '.join(['float']*3),
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help = 'origin of grid')
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group.add_option('-g',
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'--grid',
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dest = 'grid',
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type = 'int', nargs = 3, metavar = ' '.join(['int']*3),
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help = 'a,b,c grid of hexahedral box [auto]')
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group.add_option('-s',
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'--size',
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dest = 'size',
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type = 'float', nargs = 3, metavar=' '.join(['float']*3),
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help = 'x,y,z size of hexahedral box [auto]')
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group.add_option('-o',
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'--origin',
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dest = 'origin',
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type = 'float', nargs = 3, metavar=' '.join(['float']*3),
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help = 'origin of grid')
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parser.add_option_group(group)
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group = OptionGroup(parser, "Seeds","")
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group.add_option('-p', '--position',
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dest = 'position',
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group.add_option('-p',
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'--pos', '--seedposition',
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dest = 'pos',
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type = 'string', metavar = 'string',
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help = 'column label for seed positions [%default]')
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group.add_option('-w', '--weight',
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dest = 'weight',
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type = 'string', metavar = 'string',
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help = 'column label for seed weights [%default]')
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group.add_option('-m', '--microstructure',
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dest = 'microstructure',
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type = 'string', metavar = 'string',
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help = 'column label for seed microstructures [%default]')
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group.add_option('-e', '--eulers',
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dest = 'eulers',
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type = 'string', metavar = 'string',
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help = 'column label for seed Euler angles [%default]')
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help = 'label of coordinates [%default]')
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group.add_option('-w',
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'--weight',
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dest = 'weight',
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type = 'string', metavar = 'string',
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help = 'label of weights [%default]')
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group.add_option('-m',
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'--microstructure',
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dest = 'microstructure',
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type = 'string', metavar = 'string',
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help = 'label of microstructures [%default]')
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group.add_option('-e',
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'--eulers',
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dest = 'eulers',
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type = 'string', metavar = 'string',
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help = 'label of Euler angles [%default]')
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group.add_option('--axes',
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dest = 'axes',
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type = 'string', nargs = 3, metavar = ' '.join(['string']*3),
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help = 'orientation coordinate frame in terms of position coordinate frame')
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dest = 'axes',
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type = 'string', nargs = 3, metavar = ' '.join(['string']*3),
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help = 'orientation coordinate frame in terms of position coordinate frame')
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parser.add_option_group(group)
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group = OptionGroup(parser, "Configuration","")
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group.add_option('--homogenization',
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dest = 'homogenization',
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type = 'int', metavar = 'int',
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help = 'homogenization index to be used [%default]')
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dest = 'homogenization',
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type = 'int', metavar = 'int',
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help = 'homogenization index to be used [%default]')
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group.add_option('--crystallite',
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dest = 'crystallite',
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type = 'int', metavar = 'int',
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help = 'crystallite index to be used [%default]')
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dest = 'crystallite',
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type = 'int', metavar = 'int',
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help = 'crystallite index to be used [%default]')
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group.add_option('--phase',
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dest = 'phase',
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type = 'int', metavar = 'int',
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help = 'phase index to be used [%default]')
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dest = 'phase',
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type = 'int', metavar = 'int',
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help = 'phase index to be used [%default]')
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parser.add_option_group(group)
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parser.set_defaults(position = 'pos',
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parser.set_defaults(pos = 'pos',
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weight = 'weight',
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microstructure = 'microstructure',
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eulers = 'eulerangles',
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eulers = 'euler',
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homogenization = 1,
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crystallite = 1,
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phase = 1,
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@ -205,7 +213,7 @@ if filenames == []: filenames = [None]
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for name in filenames:
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try: table = damask.ASCIItable(name = name,
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outname = os.path.splitext(name)[-2]+'.geom' if name else name,
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outname = os.path.splitext(name)[0]+'.geom' if name else name,
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buffered = False)
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except: continue
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damask.util.report(scriptName,name)
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@ -238,11 +246,11 @@ for name in filenames:
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info['size'][i] = float(info['grid'][i])/max(info['grid']) # normalize to grid
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remarks.append('rescaling size {} to {}...'.format({0:'x',1:'y',2:'z'}[i],info['size'][i]))
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if table.label_dimension(options.position) != 3:
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errors.append('position columns "{}" have dimension {}.'.format(options.position,
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table.label_dimension(options.position)))
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if table.label_dimension(options.pos) != 3:
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errors.append('seed positions "{}" have dimension {}.'.format(options.pos,
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table.label_dimension(options.pos)))
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else:
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labels += [options.position]
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labels += [options.pos]
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if not hasEulers: remarks.append('missing seed orientations...')
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else: labels += [options.eulers]
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@ -260,15 +268,14 @@ for name in filenames:
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# ------------------------------------------ read seeds ---------------------------------------
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table.data_readArray(labels)
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coords = table.data[:,table.label_index(options.position):table.label_index(options.position)+3]\
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* info['size']
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eulers = table.data[:,table.label_index(options.eulers ):table.label_index(options.eulers )+3]\
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if hasEulers else np.zeros(3*len(coords))
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grains = table.data[:,table.label_index(options.microstructure)].astype('i')\
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if hasGrains else 1+np.arange(len(coords))
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weights = table.data[:,table.label_index(options.weight)]\
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if hasWeights else np.zeros(len(coords))
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grainIDs = np.unique(grains).astype('i')
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coords = table.data[:,table.label_indexrange(options.pos)] * info['size']
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eulers = table.data[:,table.label_indexrange(options.eulers)] if hasEulers \
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else np.zeros(3*len(coords))
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grains = table.data[:,table.label_indexrange(options.microstructure)].astype('i') if hasGrains \
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else 1+np.arange(len(coords))
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weights = table.data[:,table.label_indexrange(options.weight)] if hasWeights \
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else np.zeros(len(coords))
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grainIDs = np.unique(grains).astype('i')
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NgrainIDs = len(grainIDs)
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# --- tessellate microstructure ------------------------------------------------------------
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@ -289,12 +296,12 @@ for name in filenames:
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if info['homogenization'] == 0: info['homogenization'] = options.homogenization
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damask.util.croak(['grid a b c: %s'%(' x '.join(map(str,info['grid']))),
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'size x y z: %s'%(' x '.join(map(str,info['size']))),
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'origin x y z: %s'%(' : '.join(map(str,info['origin']))),
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'homogenization: %i'%info['homogenization'],
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'microstructures: %i%s'%(info['microstructures'],
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(' out of %i'%NgrainIDs if NgrainIDs != info['microstructures'] else '')),
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damask.util.croak(['grid a b c: {}'.format(' x '.join(map(str,info['grid']))),
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'size x y z: {}'.format(' x '.join(map(str,info['size']))),
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'origin x y z: {}'.format(' : '.join(map(str,info['origin']))),
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'homogenization: {}'.format(info['homogenization']),
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'microstructures: {}{}'.format(info['microstructures'],
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(' out of {}'.format(NgrainIDs) if NgrainIDs != info['microstructures'] else '')),
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])
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config_header = []
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@ -302,28 +309,28 @@ for name in filenames:
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config_header += ['<microstructure>']
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for i,ID in enumerate(grainIDs):
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config_header += ['[Grain%s]'%(str(ID).zfill(formatwidth)),
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'crystallite %i'%options.crystallite,
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'(constituent)\tphase %i\ttexture %s\tfraction 1.0'%(options.phase,str(ID).rjust(formatwidth)),
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config_header += ['[Grain{}]'.format(str(ID).zfill(formatwidth)),
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'crystallite {}'.format(options.crystallite),
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'(constituent)\tphase {}\ttexture {}\tfraction 1.0'.format(options.phase,str(ID).rjust(formatwidth)),
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]
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if hasEulers:
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config_header += ['<texture>']
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for ID in grainIDs:
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eulerID = np.nonzero(grains == ID)[0][0] # find first occurrence of this grain id
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config_header += ['[Grain%s]'%(str(ID).zfill(formatwidth)),
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'(gauss)\tphi1 %g\tPhi %g\tphi2 %g\tscatter 0.0\tfraction 1.0'%tuple(eulers[eulerID])
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config_header += ['[Grain{}]'.format(str(ID).zfill(formatwidth)),
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'(gauss)\tphi1 {:g}\tPhi {:g}\tphi2 {:g}\tscatter 0.0\tfraction 1.0'.format(*eulers[eulerID])
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]
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if options.axes is not None: config_header.append('axes\t%s %s %s'%tuple(options.axes))
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if options.axes is not None: config_header.append('axes\t{} {} {}'.format(*options.axes))
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table.labels_clear()
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table.info_clear()
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table.info_append([
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scriptID + ' ' + ' '.join(sys.argv[1:]),
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"grid\ta {grid[0]}\tb {grid[1]}\tc {grid[2]}".format(grid=info['grid']),
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"size\tx {size[0]}\ty {size[1]}\tz {size[2]}".format(size=info['size']),
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"origin\tx {origin[0]}\ty {origin[1]}\tz {origin[2]}".format(origin=info['origin']),
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"homogenization\t{homog}".format(homog=info['homogenization']),
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"microstructures\t{microstructures}".format(microstructures=info['microstructures']),
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"grid\ta {}\tb {}\tc {}".format(*info['grid']),
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"size\tx {}\ty {}\tz {}".format(*info['size']),
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"origin\tx {}\ty {}\tz {}".format(*info['origin']),
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"homogenization\t{}".format(info['homogenization']),
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"microstructures\t{}".format(info['microstructures']),
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config_header,
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])
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table.head_write()
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