166 lines
7.8 KiB
Python
Executable File
166 lines
7.8 KiB
Python
Executable File
#!/usr/bin/env python2.7
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# -*- coding: UTF-8 no BOM -*-
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import os,sys,math
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import numpy as np
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from optparse import OptionParser
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import damask
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scriptName = os.path.splitext(os.path.basename(__file__))[0]
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scriptID = ' '.join([scriptName,damask.version])
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oversampling = 2.
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#--------------------------------------------------------------------------------------------------
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# MAIN
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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=damask.extendableOption, usage='%prog option(s) [geomfile(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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""", version = scriptID)
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parser.add_option('-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(np.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.quaternion = map(float,options.quaternion)
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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 = np.array(options.center)
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invRotation = rotation.conjugated() # rotation of gridpos into primitive coordinate system
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# --- loop over input files -------------------------------------------------------------------------
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if filenames == []: filenames = [None]
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for name in filenames:
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try:
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table = damask.ASCIItable(name = name,
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buffered = False, labeled = False)
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except: continue
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damask.util.report(scriptName,name)
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# --- interpret header ----------------------------------------------------------------------------
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table.head_read()
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info,extra_header = table.head_getGeom()
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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'%info['microstructures'],
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])
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errors = []
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if np.any(info['grid'] < 1): errors.append('invalid grid a b c.')
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if np.any(info['size'] <= 0.0): errors.append('invalid size x y z.')
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if errors != []:
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damask.util.croak(errors)
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table.close(dismiss = True)
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continue
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#--- read data ------------------------------------------------------------------------------------
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microstructure = table.microstructure_read(info['grid']) # read microstructure
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# --- do work ------------------------------------------------------------------------------------
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newInfo = {
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'microstructures': 0,
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}
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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 is not None:
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mask = (np.array(options.dimension) < 0).astype(float) # zero where positive dimension, otherwise one
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dim = abs(np.array(options.dimension)) # dimensions of primitive body
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pos = np.zeros(3,dtype='float')
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# hiresPrimitive = np.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(np.arange(-dim[0]/oversampling,(dim[0]+1)/oversampling,1./oversampling)):
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for j,pos[1] in enumerate(np.arange(-dim[1]/oversampling,(dim[1]+1)/oversampling,1./oversampling)):
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for k,pos[2] in enumerate(np.arange(-dim[2]/oversampling,(dim[2]+1)/oversampling,1./oversampling)):
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gridpos = np.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 np.dot(mask*primPos/dim,mask*primPos/dim) <= 0.25 and \
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np.all(abs((1.-mask)*primPos/dim) <= 0.5): # inside ellipsoid and inside box
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microstructure[int((gridpos[0]+options.center[0])%info['grid'][0]),
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int((gridpos[1]+options.center[1])%info['grid'][1]),
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int((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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damask.util.croak('--> microstructures: %i'%newInfo['microstructures'])
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#--- write header ---------------------------------------------------------------------------------
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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=newInfo['microstructures']),
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extra_header
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])
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table.labels_clear()
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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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table.close()
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