fixed small bug ('theTable' instead of 'table') and simplified
This commit is contained in:
Martin Diehl
parent
06988353ee
commit
1ba7cbb046
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@ -1,45 +1,27 @@
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#!/usr/bin/env python
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# -*- coding: UTF-8 no BOM -*-
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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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import os,re,sys,math,string
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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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scriptID = '$Id$'
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scriptName = scriptID.split()[1]
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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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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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code inspired by http://stackoverflow.com/questions/1827489/np-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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lens = np.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 = np.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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arr2 = np.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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@ -48,9 +30,9 @@ def meshgrid2(*arrs):
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return tuple(ans)
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#--------------------------------------------------------------------------------------------------
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# --------------------------------------------------------------------
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# MAIN
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#--------------------------------------------------------------------------------------------------
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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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@ -68,11 +50,11 @@ mappings = {
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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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parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
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Generate geometry description and material configuration by standard Voronoi tessellation of given seeds file.
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""" + string.replace(scriptID,'\n','\\n')
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)
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""", version = scriptID)
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parser.add_option('-g', '--grid', dest='grid', type='int', nargs = 3, metavar = 'int int int', \
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help='a,b,c grid of hexahedral box [from seeds file]')
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@ -87,8 +69,8 @@ parser.add_option('--crystallite', dest='crystallite', type='int', metavar = 'in
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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.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(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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@ -119,14 +101,14 @@ 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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theTable = damask.ASCIItable(file['input'],file['output'],buffered = False)
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theTable.head_read()
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table = damask.ASCIItable(file['input'],file['output'],buffered = False)
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table.head_read()
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labels = ['x','y','z']
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index = 0
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hasEulers = numpy.all(theTable.labels_index(['phi1','Phi','phi2'])) != -1
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hasGrains = theTable.labels_index('microstructure') != -1
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hasEulers = np.all(table.labels_index(['phi1','Phi','phi2'])) != -1
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hasGrains = table.labels_index('microstructure') != -1
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if hasEulers:
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labels += ['phi1','Phi','phi2']
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@ -140,18 +122,18 @@ for file in files:
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grainCol = index
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theTable.data_readArray(labels)
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coords = theTable.data[:,0:3]
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eulers = theTable.data[:,eulerCol:eulerCol+3] if hasEulers else numpy.zeros(3*len(coords))
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grain = theTable.data[:,grainCol] if hasGrains else 1+numpy.arange(len(eulers))
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grainIDs = numpy.unique(grain).astype('i')
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table.data_readArray(labels)
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coords = table.data[:,0:3]
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eulers = table.data[:,eulerCol:eulerCol+3] if hasEulers else np.zeros(3*len(coords))
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grain = table.data[:,grainCol] if hasGrains else 1+np.arange(len(eulers))
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grainIDs = np.unique(grain).astype('i')
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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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'grid': np.zeros(3,'i'),
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'size': np.array(options.size),
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'origin': np.zeros(3,'d'),
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'microstructures': 0,
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'homogenization': options.homogenization,
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}
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@ -160,7 +142,7 @@ for file in files:
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}
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extra_header = []
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for header in theTable.info:
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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
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for synonym,alternatives in synonyms.iteritems():
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@ -180,7 +162,7 @@ for file in files:
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info['microstructures'] = len(grainIDs)
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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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info['grid'] = np.array(options.grid)
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for i in xrange(3):
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if info['size'][i] <= 0.0: # any invalid size?
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@ -193,10 +175,10 @@ for file in files:
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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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if numpy.any(info['grid'] < 1):
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if np.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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if np.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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if info['microstructures'] == 0:
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@ -218,22 +200,22 @@ for file in files:
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file['output'].write('\n<texture>\n')
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for i in grainIDs:
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eulerID = numpy.nonzero(grain == i)[0][0] # find first occurrence of this grain id
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eulerID = np.nonzero(grain == i)[0][0] # find first occurrence of this grain id
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file['output'].write('\n[Grain%s]\n'%(str(i).zfill(formatwidth)) + \
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'(gauss)\tphi1 %g\tPhi %g\tphi2 %g\tscatter 0.0\tfraction 1.0\n'%(eulers[0,eulerID],
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eulers[1,eulerID],
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eulers[2,eulerID]))
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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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x = (np.arange(info['grid'][0])+0.5)*info['size'][0]/info['grid'][0]
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y = (np.arange(info['grid'][1])+0.5)*info['size'][1]/info['grid'][1]
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z = (np.arange(info['grid'][2])+0.5)*info['size'][2]/info['grid'][2]
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undeformed = np.vstack(map(np.ravel, meshgrid2(x, y, z)))
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file['croak'].write('tessellating...\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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np.eye(3),\
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undeformed,coords)//3**3 + 1 # floor division to kill periodic images
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indices = grain[indices-1]
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@ -246,9 +228,9 @@ for file in files:
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' grains mapped.\n')
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#--- write header ---------------------------------------------------------------------------------
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theTable.labels_clear()
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theTable.info_clear()
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theTable.info_append(extra_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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@ -256,12 +238,12 @@ for file in files:
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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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theTable.head_write()
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table.head_write()
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# --- write microstructure information ------------------------------------------------------------
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formatwidth = 1+int(math.log10(newInfo['microstructures']))
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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),delimiter=' ')
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table.data = indices.reshape(info['grid'][1]*info['grid'][2],info['grid'][0])
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table.data_writeArray('%%%ii'%(formatwidth),delimiter=' ')
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#--- output finalization --------------------------------------------------------------------------
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