script to shift (physical) origin of geometry file and/or shift microstructure indices by fixed amount and substitute individual indices by other ones.
This commit is contained in:
Philip Eisenlohr
parent
66e38606f0
commit
b76fee325b
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#!/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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from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
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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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# ----------------------- 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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'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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'origin': lambda x: float(x),
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'homogenization': 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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translate microstructure indices (shift or substitute) and/or geometry origin.
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""" + string.replace('$Id$','\n','\\n')
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)
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parser.add_option('-o', '--origin', dest='origin', type='float', nargs = 3, \
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help='offset from old to new origin of grid', metavar='<x y z>')
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parser.add_option('-m', '--microstructure', dest='microstructure', type='int', \
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help='offset from old to new microstructure indices', metavar='<int>')
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parser.add_option('-s', '--substitute', action='extend', dest='substitute', type='string', \
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help='substitutions of microstructure indices from,to,from,to,...', metavar='<list>')
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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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parser.set_defaults(origin = [0.0,0.0,0.0])
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parser.set_defaults(microstructure = 0)
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parser.set_defaults(substitute = [])
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parser.set_defaults(twoD = False)
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(options, filenames) = parser.parse_args()
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sub = {}
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for i in xrange(len(options.substitute)/2): # split substitution list into "from" -> "to"
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sub[int(options.substitute[i*2])] = int(options.substitute[i*2+1])
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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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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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# ------------------------------------------ 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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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 = [firstline]+[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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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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'origin': [0.0,0.0,0.0],
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'homogenization': 1,
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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] 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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if info['resolution'] == [0,0,0]:
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print 'no resolution info found.'
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continue
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if info['dimension'] == [0.0,0.0,0.0]:
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print 'no dimension info found.'
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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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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]+options.origin[0],
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info['origin'][1]+options.origin[1],
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info['origin'][2]+options.origin[2]))
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new_header.append("homogenization\t%i\n"%info['homogenization'])
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# ------------------------------------------ assemble header ---------------------------------------
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output = '%i\theader\n'%(len(new_header))
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output += ''.join(new_header)
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file['output'].write(output)
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# ------------------------------------------ process input ---------------------------------------
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N = info['resolution'][0]*info['resolution'][1]*info['resolution'][2]
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microstructure = numpy.zeros(N,'i')
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i = 0
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for line in content:
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d = map(int,line.split())
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s = len(d)
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microstructure[i:i+s] = d # read microstructure indices
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i += s
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for i in xrange(N):
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if microstructure[i] in sub: microstructure[i] = sub[microstructure[i]] # substitute microstructure indices
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microstructure += options.microstructure # shift microstructure indices
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formatwidth = int(math.floor(math.log10(microstructure.max()+1)))
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i = 0
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for z in xrange(info['resolution'][2]):
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for y in xrange(info['resolution'][1]):
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output = {True:' ',False:'\n'}[options.twoD].join(map(lambda x: ('%%%ii'%formatwidth)%x, microstructure[i:i+info['resolution'][0]])) + '\n'
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file['output'].write(output)
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i += info['resolution'][0]
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# ------------------------------------------ output finalization ---------------------------------------
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if file['name'] != 'STDIN':
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file['output'].close()
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os.rename(file['name']+'_tmp',file['name'])
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@ -83,15 +83,14 @@ bin_link = { \
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'patchFromReconstructedBoundaries.py',
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'spectral_geomCheck.py',
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'spectral_geomMultiply.py',
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'spectral_geomCrop.py',
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'spectral_geomCanvas.py',
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'spectral_minimalSurface.py',
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'spectral_vicinityOffset.py',
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'spectral_ang2geom.py',
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'spectral_randomSeeding.py',
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'spectral_layeredGeom.py',
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'spectral_geomPack.py',
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'spectral_geomUnpack.py',
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'spectral_geomTranslate.py',
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'spectral_voronoiTessellation.py',
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'OIMang_hex2cub.py',
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],
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