186 lines
7.5 KiB
Python
Executable File
186 lines
7.5 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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# ----------------------- 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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Changes the (three-dimensional) canvas of a spectral geometry description.
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""" + string.replace('$Id$','\n','\\n')
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)
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parser.add_option('-b', '--box', dest='resolution', type='int', nargs = 3, \
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help='resolution of new canvas (a,b,c) %default')
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parser.add_option('-o', '--offset', dest='offset', type='int', nargs = 3, \
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help='offset from old to new origin of grid %default')
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parser.add_option('-f', '--fill', dest='fill', type='int', \
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help='(background) canvas grain index')
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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(resolution = [0,0,0])
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parser.set_defaults(offset = [0,0,0])
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parser.set_defaults(twoD = False)
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parser.set_defaults(fill = 0)
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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',
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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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# 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': numpy.array(options.resolution),
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'dimension': numpy.array([0.0,0.0,0.0]),
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'origin': numpy.array([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 options.resolution == [0,0,0]:
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options.resolution = info['resolution']
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if info['resolution'].all() == 0:
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file['croak'].write('no resolution 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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file['croak'].write('no dimension info found.\n')
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continue
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file['croak'].write('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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'homogenization: %i\n'%info['homogenization'])
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new_header.append("resolution\ta %i\tb %i\tc %i\n"%(
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options.resolution[0],
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options.resolution[1],
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options.resolution[2],))
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new_header.append("dimension\tx %f\ty %f\tz %f\n"%(
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info['dimension'][0]/info['resolution'][0]*options.resolution[0],
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info['dimension'][1]/info['resolution'][1]*options.resolution[1],
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info['dimension'][2]/info['resolution'][2]*options.resolution[2],))
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new_header.append("origin\tx %f\ty %f\tz %f\n"%(
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info['origin'][0]+info['dimension'][0]/info['resolution'][0]*options.offset[0],
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info['origin'][1]+info['dimension'][1]/info['resolution'][1]*options.offset[1],
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info['origin'][2]+info['dimension'][2]/info['resolution'][2]*options.offset[2],))
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new_header.append("homogenization\t%i\n"%info['homogenization'])
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microstructure = numpy.zeros(info['resolution'],'i')
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i = 0
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for line in content:
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for item in map(int,line.split()):
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microstructure[i%info['resolution'][0],
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(i/info['resolution'][0])%info['resolution'][1],
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i/info['resolution'][0] /info['resolution'][1]] = item
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i += 1
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microstructure_cropped = numpy.zeros(options.resolution,'i')
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microstructure_cropped.fill({True:options.fill,False:microstructure.max()+1}[options.fill>0])
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xindex = list(set(xrange(options.offset[0],options.offset[0]+options.resolution[0])) & set(xrange(info['resolution'][0])))
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yindex = list(set(xrange(options.offset[1],options.offset[1]+options.resolution[1])) & set(xrange(info['resolution'][1])))
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zindex = list(set(xrange(options.offset[2],options.offset[2]+options.resolution[2])) & set(xrange(info['resolution'][2])))
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translate_x = [i - options.offset[0] for i in xindex]
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translate_y = [i - options.offset[1] for i in yindex]
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translate_z = [i - options.offset[2] for i in zindex]
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microstructure_cropped[min(translate_x):(max(translate_x)+1),min(translate_y):(max(translate_y)+1),min(translate_z):(max(translate_z)+1)] = microstructure[min(xindex):(max(xindex)+1),min(yindex):(max(yindex)+1),min(zindex):(max(zindex)+1)]
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formatwidth = int(math.floor(math.log10(microstructure.max())+1))
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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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# ------------------------------------- regenerate texture information ----------------------------------
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for z in xrange(options.resolution[2]):
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for y in xrange(options.resolution[1]):
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output += {True:' ',False:'\n'}[options.twoD].join(map(lambda x: ('%%%ii'%formatwidth)%x, microstructure_cropped[:,y,z])) + '\n'
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#output += '\n'
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# ------------------------------------------ output result ---------------------------------------
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file['output'].write(output)
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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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