189 lines
8.0 KiB
Python
Executable File
189 lines
8.0 KiB
Python
Executable File
#!/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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#--------------------------------------------------------------------------------------------------
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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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}
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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',
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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,
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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': 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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content = file['input'].readlines()
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file['input'].close()
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#--- interpretate header --------------------------------------------------------------------------
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info = {
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'grid': numpy.array([0,0,0]),
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'size': numpy.array([0.0,0.0,0.0]),
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'origin': numpy.zeros(3,'d'),
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'microstructures': 0,
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'homogenization': 0
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}
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newInfo = {
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'origin': numpy.zeros(3,'d'),
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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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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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else:
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new_header.append(header)
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if numpy.all(info['grid'] == 0):
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file['croak'].write('no grid info found.\n')
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continue
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if numpy.all(info['size'] == 0.0):
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file['croak'].write('no size info found.\n')
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continue
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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\n'%info['microstructures'])
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#--- process input --------------------------------------------------------------------------------
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N = info['grid'][0]*info['grid'][1]*info['grid'][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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#--- assemble header and report changes -----------------------------------------------------------
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newInfo['origin'] = info['origin'] + options.origin
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newInfo['microstructures'] = microstructure.max()
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if (any(newInfo['origin'] != info['origin'])):
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file['croak'].write('--> origin x y z: %s\n'%(' : '.join(map(str,newInfo['origin']))))
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if (newInfo['microstructures'] != info['microstructures']):
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file['croak'].write('--> microstructures: %i\n'%newInfo['microstructures'])
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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"%(
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newInfo['origin'][0],newInfo['origin'][1],newInfo['origin'][2],))
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new_header.append("microstructures\t%i\n"%newInfo['microstructures'])
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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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#--- write new data -------------------------------------------------------------------------------
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i = 0
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for z in xrange(info['grid'][2]):
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for y in xrange(info['grid'][1]):
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output = {True:' ',False:'\n'}[options.twoD].join(map(lambda x: ('%%%ii'%formatwidth)%x,
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microstructure[i:i+info['grid'][0]])) + '\n'
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file['output'].write(output)
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i += info['grid'][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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