232 lines
11 KiB
Python
Executable File
232 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,string,re,math,numpy
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import damask
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from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
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scriptID = '$Id: geom_addPrimitive.py 3412 2014-08-22 16:58:53Z MPIE\m.diehl $'
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scriptName = scriptID.split()[1]
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oversampling = 2.
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#--------------------------------------------------------------------------------------------------
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class extendedOption(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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synonyms = {
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'grid': ['resolution'],
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'size': ['dimension'],
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}
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identifiers = {
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'grid': ['a','b','c'],
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'size': ['x','y','z'],
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'origin': ['x','y','z'],
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}
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mappings = {
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'grid': lambda x: int(x),
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'size': lambda x: float(x),
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'origin': lambda x: float(x),
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'homogenization': lambda x: int(x),
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'microstructures': lambda x: int(x),
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}
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parser = OptionParser(option_class=extendedOption, usage='%prog options [file[s]]', description = """
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Positions a geometric object within the (three-dimensional) canvas of a spectral geometry description.
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Depending on the sign of the dimension parameters, these objects can be boxes, cylinders, or ellipsoids.
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""" + string.replace(scriptID,'\n','\\n')
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)
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parser.add_option('-o', '--origin',
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'-c', '--center', dest='center', type='int', nargs = 3, metavar=' '.join(['int']*3),
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help='a,b,c origin of primitive %default')
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parser.add_option('-d', '--dimension', dest='dimension', type='int', nargs = 3, metavar=' '.join(['int']*3),
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help='a,b,c extension of hexahedral box; negative values are diameters')
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parser.add_option('-f', '--fill', dest='fill', type='int', metavar = 'int',
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help='grain index to fill primitive. "0" selects maximum microstructure index + 1 [%default]')
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parser.add_option('-q', '--quaternion', dest='quaternion', type='float', nargs = 4, metavar=' '.join(['float']*4),
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help = 'rotation of primitive as quaternion')
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parser.add_option('-a', '--angleaxis', dest='angleaxis', nargs = 4, metavar=' '.join(['float']*4),
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help = 'rotation of primitive as angle and axis')
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parser.add_option( '--degrees', dest='degrees', action='store_true',
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help = 'angle is given in degrees [%default]')
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parser.set_defaults(center = [0,0,0],
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fill = 0,
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quaternion = [],
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angleaxis = [],
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degrees = False,
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)
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(options, filenames) = parser.parse_args()
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if options.angleaxis != []:
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options.angleaxis = map(float,options.angleaxis)
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rotation = damask.Quaternion().fromAngleAxis(numpy.radians(options.angleaxis[0]) if options.degrees else options.angleaxis[0],
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options.angleaxis[1:4]).conjugated()
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elif options.quaternion != []:
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options.rotation = map(float,options.rotation)
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rotation = damask.Quaternion(options.quaternion).conjugated()
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else:
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rotation = damask.Quaternion().conjugated()
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options.center = numpy.array(options.center)
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invRotation = rotation.conjugated() # rotation of gridpos into primitive coordinate system
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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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table = damask.ASCIItable(file['input'],file['output'],labels = False)
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table.head_read()
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#--- interpret header ----------------------------------------------------------------------------
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info = {
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'grid': numpy.zeros(3,'i'),
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'size': numpy.zeros(3,'d'),
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'origin': numpy.zeros(3,'d'),
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'homogenization': 0,
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'microstructures': 0,
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}
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newInfo = {
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'grid': numpy.zeros(3,'i'),
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'origin': numpy.zeros(3,'d'),
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'microstructures': 0,
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}
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extra_header = []
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for header in table.info:
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headitems = map(str.lower,header.split())
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if len(headitems) == 0: continue # skip blank lines
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for synonym,alternatives in synonyms.iteritems():
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if headitems[0] in alternatives: headitems[0] = synonym
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if headitems[0] in mappings.keys():
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if headitems[0] in identifiers.keys():
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for i in xrange(len(identifiers[headitems[0]])):
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info[headitems[0]][i] = \
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mappings[headitems[0]](headitems[headitems.index(identifiers[headitems[0]][i])+1])
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else:
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info[headitems[0]] = mappings[headitems[0]](headitems[1])
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else:
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extra_header.append(header)
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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'%info['microstructures'])
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if numpy.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 numpy.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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#--- read data ------------------------------------------------------------------------------------
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microstructure = numpy.zeros(info['grid'].prod(),'i') # initialize as flat array
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i = 0
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while table.data_read():
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items = table.data
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if len(items) > 2:
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if items[1].lower() == 'of': items = [int(items[2])]*int(items[0])
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elif items[1].lower() == 'to': items = xrange(int(items[0]),1+int(items[2]))
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else: items = map(int,items)
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else: items = map(int,items)
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s = len(items)
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microstructure[i:i+s] = items
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i += s
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#--- do work ------------------------------------------------------------------------------------
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if options.fill == 0:
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options.fill = microstructure.max()+1
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microstructure = microstructure.reshape(info['grid'],order='F')
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if options.dimension != None:
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mask = (numpy.array(options.dimension) < 0).astype(float) # zero where positive dimension, otherwise one
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dim = abs(numpy.array(options.dimension)) # dimensions of primitive body
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pos = numpy.zeros(3,dtype='float')
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# hiresPrimitive = numpy.zeros((2*dim[0],2*dim[1],2*dim[2],3)) # primitive discretized at twice the grid resolution
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for i,pos[0] in enumerate(numpy.arange(-dim[0]/oversampling,(dim[0]+1)/oversampling,1./oversampling)):
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for j,pos[1] in enumerate(numpy.arange(-dim[1]/oversampling,(dim[1]+1)/oversampling,1./oversampling)):
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for k,pos[2] in enumerate(numpy.arange(-dim[2]/oversampling,(dim[2]+1)/oversampling,1./oversampling)):
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gridpos = numpy.floor(rotation*pos) # rotate and lock into spacial grid
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primPos = invRotation*gridpos # rotate back to primitive coordinate system
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if numpy.dot(mask*primPos/dim,mask*primPos/dim) <= 0.25 and \
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numpy.all(abs((1.-mask)*primPos/dim) <= 0.5): # inside ellipsoid and inside box
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microstructure[(gridpos[0]+options.center[0])%info['grid'][0],
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(gridpos[1]+options.center[1])%info['grid'][1],
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(gridpos[2]+options.center[2])%info['grid'][2]] = options.fill # assign microstructure index
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newInfo['microstructures'] = microstructure.max()
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#--- report ---------------------------------------------------------------------------------------
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if (newInfo['microstructures'] != info['microstructures']):
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file['croak'].write('--> microstructures: %i\n'%newInfo['microstructures'])
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#--- write header ---------------------------------------------------------------------------------
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table.labels_clear()
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table.info_clear()
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table.info_append(extra_header+[
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scriptID + ' ' + ' '.join(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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"homogenization\t%i"%info['homogenization'],
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"microstructures\t%i"%(newInfo['microstructures']),
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])
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table.head_write()
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table.output_flush()
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# --- write microstructure information ------------------------------------------------------------
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formatwidth = int(math.floor(math.log10(microstructure.max())+1))
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table.data = microstructure.reshape((info['grid'][0],info['grid'][1]*info['grid'][2]),order='F').transpose()
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table.data_writeArray('%%%ii'%(formatwidth),delimiter=' ')
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#--- output finalization --------------------------------------------------------------------------
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if file['name'] != 'STDIN':
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table.input_close()
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table.output_close()
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os.rename(file['name']+'_tmp',file['name'])
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