switched to new keywords "grid" and "size", still reads the old "resolution" and "dimension" but writes the new ones
This commit is contained in:
Martin Diehl
parent
964b0d7839
commit
0b1033d63a
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@ -1,5 +1,6 @@
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#!/usr/bin/env python
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# -*- coding: utf-8 -*-
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import os,sys,math,string,re,numpy, damask
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from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
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@ -23,16 +24,14 @@ class extendedOption(Option):
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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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identifiers = {
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'resolution': ['a','b','c'],
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'grid': ['a','b','c'],
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}
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mappings = {
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'resolution': lambda x: int(x),
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'grid': lambda x: int(x),
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'grains': lambda x: int(x),
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}
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@ -41,24 +40,24 @@ Generate geometry description and material configuration by standard Voronoi tes
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""" + string.replace('$Id$','\n','\\n')
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)
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parser.add_option('-r', '--resolution', dest='resolution', type='int', nargs = 3, \
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help='a,b,c resolution of periodic box')
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parser.add_option('-d', '--dimension', dest='dimension', type='float', nargs = 3, \
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help='x,y,z dimension of periodic box')
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parser.add_option('-g', '--grid', dest='grid', type='int', nargs = 3, \
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help='a,b,c grid of hexahedral box [from seed file]')
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parser.add_option('-s', '--size', dest='size', type='float', nargs = 3, \
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help='x,y,z size of hexahedral box [1.0 along largest grid point number]')
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parser.add_option('--homogenization', dest='homogenization', type='int', \
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help='homogenization index to be used')
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help='homogenization index to be used [%default]')
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parser.add_option('--phase', dest='phase', type='int', \
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help='phase index to be used')
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help='phase index to be used [%default]')
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parser.add_option('--crystallite', dest='crystallite', type='int', \
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help='crystallite index to be used')
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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')
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help='output material configuration [%default]')
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parser.add_option('-2', '--twodimensional', dest='twoD', action='store_true', \
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help='output geom file with two-dimensional data arrangement')
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help='output geom file with two-dimensional data arrangement [%default]')
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parser.set_defaults(resolution = [0,0,0])
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parser.set_defaults(dimension = [0.0,0.0,0.0])
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parser.set_defaults(grid = [0,0,0])
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parser.set_defaults(size = [0.0,0.0,0.0])
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parser.set_defaults(homogenization = 1)
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parser.set_defaults(phase = 1)
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parser.set_defaults(crystallite = 1)
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@ -105,8 +104,8 @@ for file in files:
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file['input'].close()
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info = {'grains': 0,
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'resolution': numpy.array([0,0,0]),
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'dimension': numpy.array(options.dimension),
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'grid': numpy.array([0,0,0]),
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'size': numpy.array(options.size),
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'origin': numpy.array([0.0,0.0,0.0]),
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'homogenization': options.homogenization,
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}
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@ -114,6 +113,7 @@ for file in files:
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new_header = []
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for header in headers:
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headitems = map(str.lower,header.split())
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if headitems[0] == 'resolution': headitems[0] = 'grid'
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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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@ -129,39 +129,26 @@ for file in files:
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file['croak'].write('grain data not matching grain count...\n')
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info['grains'] = min(info['grains'],len(content))
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if 0 not in options.resolution: # user-specified resolution
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info['resolution'] = numpy.array(options.resolution)
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if 0 not in options.grid: # user-specified grid
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info['grid'] = numpy.array(options.grid)
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if numpy.all(info['resolution'] == 0):
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file['croak'].write('no resolution info found.\n')
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if numpy.any(info['grid'] < 1):
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file['croak'].write('no valid grid info found.\n')
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continue
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twoD = info['resolution'][2] < 2
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twoD = info['grid'][2] < 2
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for i in xrange(3):
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if info['dimension'][i] <= 0.0: # any invalid dimension?
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info['dimension'][i] = float(info['resolution'][i])/max(info['resolution'])
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file['croak'].write('rescaling dimension %i...\n'%i)
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if info['size'][i] <= 0.0: # any invalid size?
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info['size'][i] = float(info['grid'][i])/max(info['grid'])
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file['croak'].write('rescaling size %i...\n'%i)
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file['croak'].write('grains: %i\n'%info['grains'] + \
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'resolution: %s\n'%(' x '.join(map(str,info['resolution']))) + \
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'dimension: %s\n'%(' x '.join(map(str,info['dimension']))) + \
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'origin: %s\n'%(' : '.join(map(str,info['origin']))) + \
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file['croak'].write('grains to map: %i\n'%info['grains'] + \
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'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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new_header.append("resolution\ta %i\tb %i\tc %i\n"%(
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info['resolution'][0],
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info['resolution'][1],
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info['resolution'][2],))
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new_header.append("dimension\tx %f\ty %f\tz %f\n"%(
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info['dimension'][0],
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info['dimension'][1],
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info['dimension'][2],))
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new_header.append("origin\tx %f\ty %f\tz %f\n"%(
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info['origin'][0],
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info['origin'][1],
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info['origin'][2],))
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new_header.append("homogenization\t%i\n"%info['homogenization'])
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# -------------------------------------- prepare data ----------------------------------
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@ -170,12 +157,12 @@ for file in files:
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eulers = numpy.zeros((3,info['grains']),'d')
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for i in xrange(info['grains']):
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coords[:,i] = map(float,content[i].split()[:3])*info['dimension']
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coords[:,i] = map(float,content[i].split()[:3])*info['size']
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eulers[:,i] = map(float,content[i].split()[3:6])
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# -------------------------------------- switch according to task ----------------------------------
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if options.config:
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if options.config: # write config file
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file['output'].write('<microstructure>\n')
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for i in xrange(info['grains']):
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file['output'].write('\n[Grain%s]\n'%(str(i+1).zfill(formatwidth)) + \
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@ -187,40 +174,56 @@ for file in files:
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file['output'].write('\n[Grain%s]\n'%(str(i+1).zfill(formatwidth)) + \
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'(gauss)\tphi1 %g\tPhi %g\tphi2 %g\tscatter 0.0\tfraction 1.0\n'%(eulers[0,i],eulers[1,i],eulers[2,i]))
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else:
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file['output'].write('%i\theader\n'%(len(new_header)) + ''.join(new_header))
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N = info['resolution'].prod()
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shift = 0.5*info['dimension']/info['resolution'] # shift by half of side length to center of element
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else: # write geometry file
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N = info['grid'].prod()
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shift = 0.5*info['size']/info['grid'] # shift by half of side length to center of element
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undeformed = numpy.zeros((3,N),'d')
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for i in xrange(N):
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undeformed[0,i] = info['dimension'][0]\
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* float(i % info['resolution'][0])\
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/float(info['resolution'][0])
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undeformed[1,i] = info['dimension'][1]\
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* float(i//info['resolution'][0] % info['resolution'][1])\
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/float(info['resolution'][1])
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undeformed[2,i] = info['dimension'][2]\
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* float(i//info['resolution'][0]//info['resolution'][1] % info['resolution'][2])\
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/float(info['resolution'][2])
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undeformed[0,i] = info['size'][0]\
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* float(i % info['grid'][0])\
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/float(info['grid'][0])
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undeformed[1,i] = info['size'][1]\
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* float(i//info['grid'][0] % info['grid'][1])\
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/float(info['grid'][1])
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undeformed[2,i] = info['size'][2]\
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* float(i//info['grid'][0]//info['grid'][1] % info['grid'][2])\
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/float(info['grid'][2])
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undeformed[:,i] += shift
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indices = damask.core.math.periodicNearestNeighbor(\
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info['dimension'],\
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info['size'],\
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numpy.eye(3),\
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undeformed,coords)//3**3 + 1 # floor division to kill periodic images
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for n in xrange(info['resolution'][1:3].prod()): # loop over 2nd and 3rd dimension
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file['output'].write({ True: ' ',
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False:'\n'}[options.twoD].\
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join(map(lambda x: str(x).rjust(formatwidth),\
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indices[n*info['resolution'][0]:(n+1)*info['resolution'][0]]))+'\n')
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missing = 0
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for i in xrange(info['grains']):
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if i+1 not in indices: missing += 1
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file['croak'].write({True:'all',False:'only'}[missing == 0] + ' %i grains mapped.\n'%(info['grains']-missing))
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new_header.append("grid\ta %i\tb %i\tc %i\n"%(
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info['grid'][0],
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info['grid'][1],
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info['grid'][2],))
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new_header.append("size\tx %f\ty %f\tz %f\n"%(
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info['size'][0],
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info['size'][1],
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info['size'][2],))
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new_header.append("origin\tx %f\ty %f\tz %f\n"%(
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info['origin'][0],
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info['origin'][1],
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info['origin'][2],))
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new_header.append("microstructures\t%i\n"%(info['grains']-missing))
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new_header.append("homogenization\t%i\n"%info['homogenization'])
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file['output'].write('%i\theader\n'%(len(new_header)) + ''.join(new_header))
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for n in xrange(info['grid'][1:3].prod()): # loop over 2nd and 3rd size
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file['output'].write({ True: ' ',
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False:'\n'}[options.twoD].\
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join(map(lambda x: str(x).rjust(formatwidth),\
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indices[n*info['grid'][0]:(n+1)*info['grid'][0]]))+'\n')
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# ------------------------------------------ output finalization ---------------------------------------
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if file['name'] != 'STDIN':
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@ -27,16 +27,16 @@ class extendedOption(Option):
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# ----------------------- MAIN -------------------------------
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identifiers = {
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'resolution': ['a','b','c'],
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'dimension': ['x','y','z'],
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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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'resolution': lambda x: int(x),
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'dimension': lambda x: float(x),
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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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'maxmicrostructure': lambda x: int(x),
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'microstructures': lambda x: int(x),
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}
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@ -51,19 +51,26 @@ compress geometry files with ranges "a to b" and/or multiples "n of x".
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files = []
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if filenames == []:
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files.append({'name':'STDIN', 'input':sys.stdin, 'output':sys.stdout})
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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, 'input':open(name), 'output':open(name+'_tmp','w')})
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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': print file['name']
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# get labels by either read the first row, or - if keyword header is present - the last line of the header
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if file['name'] != 'STDIN': file['croak'].write(file['name']+'\n')
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# get labels by either read the first row, or - if keyword header is present - the last line of the header
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firstline = file['input'].readline()
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m = re.search('(\d+)\s*head', firstline.lower())
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if m:
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@ -76,16 +83,18 @@ for file in files:
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content = file['input'].readlines()
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file['input'].close()
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info = {'resolution': [0,0,0],
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'dimension': [0.0,0.0,0.0],
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info = {'grid': [0,0,0],
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'size': [0.0,0.0,0.0],
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'origin': [0.0,0.0,0.0],
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'homogenization': 1,
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'maxmicrostructure': 0,
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'microstructures': 0,
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}
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new_header = []
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for header in headers:
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headitems = map(str.lower,header.split())
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if headitems[0] == 'resolution': headitems[0] = 'grid'
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if headitems[0] == 'dimension': headitems[0] = 'size'
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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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@ -94,33 +103,34 @@ for file in files:
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else:
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info[headitems[0]] = mappings[headitems[0]](headitems[1])
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if info['resolution'] == [0,0,0]:
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sys.stderr.write('no resolution info found.\n')
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if info['grid'] == [0,0,0]:
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file['croak'].write('no grid info found.\n')
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continue
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if info['dimension'] == [0.0,0.0,0.0]:
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sys.stderr.write('no dimension info found.\n')
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if info['size'] == [0.0,0.0,0.0]:
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file['croak'].write('no size info found.\n')
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continue
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if file['name'] != 'STDIN':
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print 'resolution: %s'%(' x '.join(map(str,info['resolution'])))
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print 'dimension: %s'%(' x '.join(map(str,info['dimension'])))
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print 'origin: %s'%(' : '.join(map(str,info['origin'])))
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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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new_header.append("resolution\ta %i\tb %i\tc %i\n"%(
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info['resolution'][0],
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info['resolution'][1],
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info['resolution'][2],))
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new_header.append("dimension\tx %f\ty %f\tz %f\n"%(
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info['dimension'][0],
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info['dimension'][1],
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info['dimension'][2]))
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new_header.append("grid\ta %i\tb %i\tc %i\n"%(
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info['grid'][0],
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info['grid'][1],
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info['grid'][2],))
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new_header.append("size\tx %f\ty %f\tz %f\n"%(
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info['size'][0],
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info['size'][1],
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info['size'][2]))
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new_header.append("origin\tx %f\ty %f\tz %f\n"%(
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info['origin'][0],
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info['origin'][1],
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info['origin'][2]))
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new_header.append("homogenization\t%i\n"%info['homogenization'])
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if info['maxmicrostructure'] > 0:
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new_header.append("maxMicrostructure\t%i\n"%info['maxmicrostructure'])
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if info['microstructures'] > 0:
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new_header.append("microstructures\t%i\n"%info['microstructures'])
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# ------------------------------------------ assemble header ---------------------------------------
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@ -27,16 +27,17 @@ class extendedOption(Option):
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# ----------------------- MAIN -------------------------------
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identifiers = {
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'resolution': ['a','b','c'],
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'dimension': ['x','y','z'],
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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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'resolution': lambda x: int(x),
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'dimension': lambda x: float(x),
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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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'maxmicrostructure': lambda x: int(x),
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'microstructures': lambda x: int(x),
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}
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@ -46,26 +47,33 @@ Unpack geometry files containing ranges "a to b" and/or "n of x" multiples (excl
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)
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parser.add_option('-2', '--twodimensional', dest='twoD', action='store_true', \
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help='output geom file with two-dimensional data arrangement')
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help='output geom file with two-dimensional data arrangement [%default]')
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parser.set_defaults(twoD = False)
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(options, filenames) = parser.parse_args()
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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', 'input':sys.stdin, 'output':sys.stdout})
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files.append({'name':'STDIN',
|
||||
'input':sys.stdin,
|
||||
'output':sys.stdout,
|
||||
'croak':sys.stderr,
|
||||
})
|
||||
else:
|
||||
for name in filenames:
|
||||
if os.path.exists(name):
|
||||
files.append({'name':name, 'input':open(name), 'output':open(name+'_tmp','w')})
|
||||
files.append({'name':name,
|
||||
'input':open(name),
|
||||
'output':open(name+'_tmp','w'),
|
||||
'croak':sys.stdout,
|
||||
})
|
||||
|
||||
# ------------------------------------------ loop over input files ---------------------------------------
|
||||
|
||||
for file in files:
|
||||
if file['name'] != 'STDIN': print file['name']
|
||||
if file['name'] != 'STDIN': file['croak'].write(file['name']+'\n')
|
||||
|
||||
# get labels by either read the first row, or - if keyword header is present - the last line of the header
|
||||
|
||||
|
|
@ -81,16 +89,18 @@ for file in files:
|
|||
content = file['input'].readlines()
|
||||
file['input'].close()
|
||||
|
||||
info = {'resolution': [0,0,0],
|
||||
'dimension': [0.0,0.0,0.0],
|
||||
info = {'grid': [0,0,0],
|
||||
'size': [0.0,0.0,0.0],
|
||||
'origin': [0.0,0.0,0.0],
|
||||
'homogenization': 1,
|
||||
'maxmicrostructure': 0,
|
||||
'microstructures': 0,
|
||||
}
|
||||
|
||||
new_header = []
|
||||
for header in headers:
|
||||
headitems = map(str.lower,header.split())
|
||||
if headitems[0] == 'resolution': headitems[0] = 'grid'
|
||||
if headitems[0] == 'dimension': headitems[0] = 'size'
|
||||
if headitems[0] in mappings.keys():
|
||||
if headitems[0] in identifiers.keys():
|
||||
for i in xrange(len(identifiers[headitems[0]])):
|
||||
|
|
@ -99,39 +109,40 @@ for file in files:
|
|||
else:
|
||||
info[headitems[0]] = mappings[headitems[0]](headitems[1])
|
||||
|
||||
if info['resolution'] == [0,0,0]:
|
||||
sys.stderr.write('no resolution info found.\n')
|
||||
if info['grid'] == [0,0,0]:
|
||||
file['croak'].write('no grid info found.\n')
|
||||
continue
|
||||
if info['dimension'] == [0.0,0.0,0.0]:
|
||||
sys.stderr.write('no dimension info found.\n')
|
||||
if info['size'] == [0.0,0.0,0.0]:
|
||||
file['croak'].write('no size info found.\n')
|
||||
continue
|
||||
|
||||
format = {True: info['resolution'][0],
|
||||
format = {True: info['grid'][0],
|
||||
False: 1}[options.twoD]
|
||||
|
||||
if file['name'] != 'STDIN':
|
||||
print 'resolution: %s'%(' x '.join(map(str,info['resolution'])))
|
||||
print 'dimension: %s'%(' x '.join(map(str,info['dimension'])))
|
||||
print 'origin: %s'%(' : '.join(map(str,info['origin'])))
|
||||
file['croak'].write('grid a b c: %s\n'%(' x '.join(map(str,info['grid']))) + \
|
||||
'size x y z: %s\n'%(' x '.join(map(str,info['size']))) + \
|
||||
'origin x y z: %s\n'%(' : '.join(map(str,info['origin']))) + \
|
||||
'homogenization: %i\n'%info['homogenization'] + \
|
||||
'microstructures: %i\n'%info['microstructures'])
|
||||
|
||||
new_header.append("resolution\ta %i\tb %i\tc %i\n"%(
|
||||
info['resolution'][0],
|
||||
info['resolution'][1],
|
||||
info['resolution'][2],))
|
||||
new_header.append("dimension\tx %f\ty %f\tz %f\n"%(
|
||||
info['dimension'][0],
|
||||
info['dimension'][1],
|
||||
info['dimension'][2]))
|
||||
new_header.append("grid\ta %i\tb %i\tc %i\n"%(
|
||||
info['grid'][0],
|
||||
info['grid'][1],
|
||||
info['grid'][2],))
|
||||
new_header.append("size\tx %f\ty %f\tz %f\n"%(
|
||||
info['size'][0],
|
||||
info['size'][1],
|
||||
info['size'][2]))
|
||||
new_header.append("origin\tx %f\ty %f\tz %f\n"%(
|
||||
info['origin'][0],
|
||||
info['origin'][1],
|
||||
info['origin'][2]))
|
||||
new_header.append("homogenization\t%i\n"%info['homogenization'])
|
||||
if info['maxmicrostructure'] > 0:
|
||||
new_header.append("maxMicrostructure\t%i\n"%info['maxmicrostructure'])
|
||||
digits = 1+int(math.log10(int(info['maxmicrostructure'])))
|
||||
if info['microstructures'] > 0:
|
||||
new_header.append("microstructures\t%i\n"%info['microstructures'])
|
||||
digits = 1+int(math.log10(int(info['microstructures'])))
|
||||
else:
|
||||
digits = 1+int(math.log10(int(info['resolution'][0]*info['resolution'][1]*info['resolution'][2])))
|
||||
digits = 1+int(math.log10(int(info['grid'][0]*info['grid'][1]*info['grid'][2])))
|
||||
|
||||
# ------------------------------------------ assemble header ---------------------------------------
|
||||
|
||||
|
|
|
|||
|
|
@ -27,12 +27,10 @@ class extendedOption(Option):
|
|||
# ----------------------- MAIN -------------------------------
|
||||
|
||||
identifiers = {
|
||||
'resolution': ['a','b','c'],
|
||||
'dimension': ['x','y','z'],
|
||||
'grid': ['a','b','c'],
|
||||
}
|
||||
mappings = {
|
||||
'resolution': lambda x: int(x),
|
||||
'dimension': lambda x: float(x),
|
||||
'grid': lambda x: int(x),
|
||||
}
|
||||
|
||||
|
||||
|
|
@ -44,18 +42,18 @@ Reports positions with random crystal orientations in seeds file format to STDOU
|
|||
|
||||
parser.add_option('-N', dest='N', type='int', \
|
||||
help='number of seed points to distribute [%default]')
|
||||
parser.add_option('-r','--resolution', dest='res', type='int', nargs=3, \
|
||||
help='Min Fourier points in x, y, z %default')
|
||||
parser.add_option('-s', '--rnd', dest='randomSeed', type='int', \
|
||||
parser.add_option('-g','--grid', dest='grid', type='int', nargs=3, \
|
||||
help='min a,b,c grid of hexahedral box %default')
|
||||
parser.add_option('-r', '--rnd', dest='randomSeed', type='int', \
|
||||
help='seed of random number generator [%default]')
|
||||
|
||||
parser.set_defaults(randomSeed = 0)
|
||||
parser.set_defaults(res = [16,16,16])
|
||||
parser.set_defaults(grid = [16,16,16])
|
||||
parser.set_defaults(N = 20)
|
||||
|
||||
(options, extras) = parser.parse_args()
|
||||
|
||||
Npoints = options.res[0]*options.res[1]*options.res[2]
|
||||
Npoints = options.grid[0]*options.grid[1]*options.grid[2]
|
||||
if options.N > Npoints:
|
||||
sys.stderr.write('Warning: more seeds than grid points at minimum resolution.\n')
|
||||
options.N = Npoints
|
||||
|
|
@ -69,14 +67,17 @@ grainEuler[1,:] = numpy.arccos(2*grainEuler[1,:]-1)*180.0/math.pi
|
|||
grainEuler[2,:] *= 360.0
|
||||
|
||||
seedpoint = numpy.random.permutation(Npoints)[:options.N]
|
||||
seeds[0,:] = (numpy.mod(seedpoint ,options.res[0])+numpy.random.random())/options.res[0]
|
||||
seeds[1,:] = (numpy.mod(seedpoint// options.res[0] ,options.res[1])+numpy.random.random())/options.res[1]
|
||||
seeds[2,:] = (numpy.mod(seedpoint//(options.res[1]*options.res[0]),options.res[2])+numpy.random.random())/options.res[2]
|
||||
seeds[0,:]=(numpy.mod(seedpoint ,options.grid[0])\
|
||||
+numpy.random.random())/options.grid[0]
|
||||
seeds[1,:]=(numpy.mod(seedpoint// options.grid[0],options.grid[1])\
|
||||
+numpy.random.random())/options.grid[1]
|
||||
seeds[2,:]=(numpy.mod(seedpoint//(options.grid[1]*options.grid[0]),options.grid[2])\
|
||||
+numpy.random.random())/options.grid[2]
|
||||
|
||||
print "4\theader"
|
||||
print "resolution\ta %i\tb %i\tc %i"%(options.res[0],options.res[1],options.res[2],)
|
||||
print "grid\ta %i\tb %i\tc %i"%(options.grid[0],options.grid[1],options.grid[2],)
|
||||
print "grains\t%i"%options.N
|
||||
print "randomSeed\t%f"%(options.randomSeed)
|
||||
print "randomSeed\t%i"%(options.randomSeed)
|
||||
print "x\ty\tz\tphi1\tPhi\tphi2"
|
||||
|
||||
numpy.savetxt(sys.stdout,numpy.transpose(numpy.concatenate((seeds,grainEuler),axis = 0)),fmt='%10.6f',delimiter='\t')
|
||||
|
|
|
|||
Loading…
Reference in New Issue