now based on damask.ASCIItable object
switched to numpy functions for grid generation --> about 20x faster.
This commit is contained in:
Philip Eisenlohr
parent
9abc9a99fc
commit
da1b4ff05b
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@ -1,7 +1,8 @@
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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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import os,sys,math,string,re,numpy,
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import damask
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from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
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#--------------------------------------------------------------------------------------------------
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@ -23,6 +24,27 @@ class extendedOption(Option):
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Option.take_action(self, action, dest, opt, value, values, parser)
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def meshgrid2(*arrs):
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'''
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code inspired by http://stackoverflow.com/questions/1827489/numpy-meshgrid-in-3d
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'''
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arrs = tuple(reversed(arrs))
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arrs = tuple(arrs)
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lens = numpy.array(map(len, arrs))
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dim = len(arrs)
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ans = []
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for i, arr in enumerate(arrs):
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slc = numpy.ones(dim,'i')
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slc[i] = lens[i]
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arr2 = numpy.asarray(arr).reshape(slc)
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for j, sz in enumerate(lens):
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if j != i:
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arr2 = arr2.repeat(sz, axis=j)
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ans.insert(0,arr2)
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return tuple(ans)
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#--------------------------------------------------------------------------------------------------
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# MAIN
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#--------------------------------------------------------------------------------------------------
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@ -51,9 +73,6 @@ parser.add_option('--crystallite', dest='crystallite', type='int', \
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help='crystallite index to be used [%default]')
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parser.add_option('-c', '--configuration', dest='config', action='store_true', \
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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 [%default]')
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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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@ -61,8 +80,7 @@ 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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parser.set_defaults(config = False)
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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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@ -87,30 +105,22 @@ else:
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for file in files:
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if file['name'] != 'STDIN': file['croak'].write(file['name']+'\n')
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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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headerlines = int(m.group(1))
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headers = [file['input'].readline() for i in range(headerlines)]
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else:
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headerlines = 1
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headers = firstline
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theTable = damask.ASCIItable(file['input'],file['output'])
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theTable.head_read()
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theData = theTable.data_asArray(['x','y','z','phi1','Phi','phi2'])
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content = file['input'].readlines()
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file['input'].close()
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#--- interprete header ----------------------------------------------------------------------------
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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.array(options.size),
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'origin': numpy.zeros(3,'d'),
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'grains': 0,
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'homogenization': 0,
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'grains': 0,
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'homogenization': options.homogenization,
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}
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new_header = []
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for header in headers:
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for header in theTable.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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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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@ -120,9 +130,9 @@ 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['grains'] != len(content):
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if info['grains'] != len(theData):
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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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info['grains'] = min(info['grains'],len(theData))
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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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@ -140,22 +150,18 @@ for file in files:
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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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sys.exit()
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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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sys.exit()
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continue
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if info['grains'] == 0:
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file['croak'].write('no grain info found.\n')
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sys.exit()
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continue
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#--- prepare data ---------------------------------------------------------------------------------
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formatwidth = 1+int(math.log10(info['grains']))
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coords = numpy.zeros((3,info['grains']),'d')
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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['size']
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eulers[:,i] = map(float,content[i].split()[3:6])
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coords = (theData[:,:3]*info['size']).transpose()
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eulers = (theData[:,3:6]).transpose()
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#--- switch according to task ---------------------------------------------------------------------
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if options.config: # write config file
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@ -170,24 +176,13 @@ 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: # write geometry file
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twoD = info['grid'][2] < 2
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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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else: # write geometry file
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x = (numpy.arange(info['grid'][0])+0.5)*info['size'][0]/info['grid'][0]
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y = (numpy.arange(info['grid'][1])+0.5)*info['size'][1]/info['grid'][1]
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z = (numpy.arange(info['grid'][2])+0.5)*info['size'][2]/info['grid'][2]
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undeformed = numpy.vstack(map(numpy.ravel, meshgrid2(x, y, z)))
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for i in xrange(N):
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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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file['croak'].write('tesselating...\n')
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indices = damask.core.math.periodicNearestNeighbor(\
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info['size'],\
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numpy.eye(3),\
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@ -198,23 +193,27 @@ for file in files:
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file['croak'].write({True:'all',False:'only'}[missing == 0] + ' %i grains mapped.\n'%(info['grains']-missing))
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#--- write header ---------------------------------------------------------------------------------
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new_header.append("$Id$ \n")
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new_header.append("grid\ta %i\tb %i\tc %i\n"%(info['grid'][0],info['grid'][1],info['grid'][2],))
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new_header.append("size\tx %f\ty %f\tz %f\n"%(info['size'][0],info['size'][1],info['size'][2],))
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new_header.append("origin\tx %f\ty %f\tz %f\n"%(info['origin'][0],info['origin'][1],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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theTable.labels_clear()
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theTable.info_clear()
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theTable.info_append([
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"$Id$",
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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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"microstructures\t%i"%(info['grains']-missing),
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"homogenization\t%i"%info['homogenization'],
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])
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theTable.head_write()
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theTable.output_flush()
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# --- write microstructure information ------------------------------------------------------------
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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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theTable.data = indices.reshape(info['grid'][1]*info['grid'][2],info['grid'][0])
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theTable.data_writeArray('%%%ii'%(formatwidth))
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#--- output finalization --------------------------------------------------------------------------
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if file['name'] != 'STDIN':
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file['input'].close()
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file['output'].close()
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os.rename(file['name']+'_tmp',os.path.splitext(file['name'])[0] + \
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{True: '_material.config',
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