grid and size for vicinityOffset, small changes for other scripts
This commit is contained in:
Martin Diehl
parent
5d8664e230
commit
a003d14824
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@ -150,7 +150,7 @@ for file in files:
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info = {'grid': [0,0,0],
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'size': [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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'homogenization': 0,
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'microstructures': 0,
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}
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@ -95,7 +95,7 @@ for file in files:
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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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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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@ -27,15 +27,16 @@ class extendedOption(Option):
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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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'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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'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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'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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'microstructures': lambda x: int(x),
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}
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@ -47,8 +48,8 @@ i.e. within the region close to a grain/phase boundary.
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parser.add_option('-v', '--vicinity', dest='vicinity', type='int', \
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help='voxel distance checked for presence of other microstructure [%default]')
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parser.add_option('-o', '--offset', dest='offset', type='int', \
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help='integer offset for tagged microstructure [%default]')
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parser.add_option('-m', '--microstructureoffset', dest='offset', type='int', \
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help='integer offset for tagged microstructure [autodetect]')
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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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@ -88,7 +89,7 @@ for file in files:
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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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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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@ -96,15 +97,20 @@ for file in files:
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content = file['input'].readlines()
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file['input'].close()
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info = {'resolution': numpy.array([0,0,0]),
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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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info = {
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'grid': numpy.zeros(3,'i'),
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'size': numpy.zeros(3,'d'),
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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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new_header = []
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new_header.append('$Id$\n')
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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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@ -112,36 +118,40 @@ for file in files:
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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['resolution'] == 0):
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file['croak'].write('no resolution info found.\n')
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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['dimension'] == 0.0):
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if numpy.all(info['size'] == 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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file['croak'].write('-- input --\n' +\
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'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'%info['microstructures'])
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microstructure = numpy.zeros(info['resolution'],'i')
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microstructure = numpy.zeros(info['grid'],'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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microstructure[i%info['grid'][0],
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(i/info['grid'][0])%info['grid'][1],
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i/info['grid'][0] /info['grid'][1]] = item
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i += 1
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formatwidth = 1+int(math.floor(math.log10(abs(microstructure.max()+options.offset))))
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if options.offset == 0:
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options.offset = microstructure.max()
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file['croak'].write('offset: %i\n'%options.offset)
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for x in xrange(info['resolution'][0]):
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for y in xrange(info['resolution'][1]):
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for z in xrange(info['resolution'][2]):
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formatwidth = 1+int(math.floor(math.log10(abs(microstructure.max()+options.offset))))
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for x in xrange(info['grid'][0]):
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for y in xrange(info['grid'][1]):
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for z in xrange(info['grid'][2]):
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me = microstructure[x,y,z]
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breaker = False
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@ -150,7 +160,7 @@ for file in files:
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for dy in xrange(-options.vicinity,options.vicinity+1):
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for dz in xrange(-options.vicinity,options.vicinity+1):
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they = microstructure[(x+dx)%info['resolution'][0],(y+dy)%info['resolution'][1],(z+dz)%info['resolution'][2]]
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they = microstructure[(x+dx)%info['grid'][0],(y+dy)%info['grid'][1],(z+dz)%info['grid'][2]]
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if they != me and they != me+options.offset: # located alien microstructure in vicinity
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microstructure[x,y,z] += options.offset # tag myself as close to aliens!
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breaker = True
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@ -160,15 +170,25 @@ for file in files:
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if breaker: break
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# ------------------------------------------ assemble header ---------------------------------------
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info['microstructures'] = microstructure.max()
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file['croak'].write('-- output --\n' +\
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'microstructures: %i\n'%info['microstructures'])
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# ------------------------------------------ assemble header ---------------------------------------
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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'][0]))
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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['microstructures'])
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new_header.append("homogenization\t%i\n"%info['homogenization'])
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output = '%i\theader\n'%(len(new_header))
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output += ''.join(new_header)
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output = ''.join(headers)
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# ------------------------------------- regenerate texture information ----------------------------------
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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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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: str(x).rjust(formatwidth), microstructure[:,y,z])) + '\n'
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output += '\n'
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