DAMASK_EICMD/processing/pre/geom_rescale.py

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#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
import os,sys,string,re,math,numpy
from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
#--------------------------------------------------------------------------------------------------
class extendedOption(Option):
#--------------------------------------------------------------------------------------------------
# used for definition of new option parser action 'extend', which enables to take multiple option arguments
# taken from online tutorial http://docs.python.org/library/optparse.html
ACTIONS = Option.ACTIONS + ("extend",)
STORE_ACTIONS = Option.STORE_ACTIONS + ("extend",)
TYPED_ACTIONS = Option.TYPED_ACTIONS + ("extend",)
ALWAYS_TYPED_ACTIONS = Option.ALWAYS_TYPED_ACTIONS + ("extend",)
def take_action(self, action, dest, opt, value, values, parser):
if action == "extend":
lvalue = value.split(",")
values.ensure_value(dest, []).extend(lvalue)
else:
Option.take_action(self, action, dest, opt, value, values, parser)
#--------------------------------------------------------------------------------------------------
# MAIN
#--------------------------------------------------------------------------------------------------
identifiers = {
'grid': ['a','b','c'],
'size': ['x','y','z'],
'origin': ['x','y','z'],
}
mappings = {
'grid': lambda x: int(x),
'size': lambda x: float(x),
'origin': lambda x: float(x),
'homogenization': lambda x: int(x),
'microstructures': lambda x: int(x),
}
parser = OptionParser(option_class=extendedOption, usage='%prog options [file[s]]', description = """
Scales a geometry description independently in x, y, and z direction in terms of grid and/or size.
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""" + string.replace('$Id$','\n','\\n')
)
parser.add_option('-g', '--grid', dest='grid', type='string', nargs = 3, \
help='a,b,c grid of hexahedral box [unchanged]')
parser.add_option('-s', '--size', dest='size', type='string', nargs = 3, \
help='x,y,z size of hexahedral box [unchanged]')
parser.add_option('-2', '--twodimensional', dest='twoD', action='store_true', \
help='output geom file with two-dimensional data arrangement [%default]')
parser.set_defaults(grid = ['0','0','0'])
parser.set_defaults(size = ['0.0','0.0','0.0'])
parser.set_defaults(twoD = False)
(options, filenames) = parser.parse_args()
#--- setup file handles ---------------------------------------------------------------------------
files = []
if filenames == []:
files.append({'name':'STDIN',
'input':sys.stdin,
'output':sys.stdout,
'croak':sys.stderr,
})
else:
for name in filenames:
if os.path.exists(name):
files.append({'name':name,
'input':open(name),
'output':open(name+'_tmp','w'),
'croak':sys.stdout,
})
#--- loop over input files ------------------------------------------------------------------------
for file in files:
if file['name'] != 'STDIN': file['croak'].write(file['name']+'\n')
firstline = file['input'].readline()
m = re.search('(\d+)\s*head', firstline.lower())
if m:
headerlines = int(m.group(1))
headers = [file['input'].readline() for i in range(headerlines)]
else:
headerlines = 1
headers = firstline
content = file['input'].readlines()
file['input'].close()
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#--- interprete header ----------------------------------------------------------------------------
info = {
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'grid': numpy.zeros(3,'i'),
'size': numpy.zeros(3,'d'),
'origin': numpy.zeros(3,'d'),
'microstructures': 0,
'homogenization': 0
}
newInfo = {
'grid': numpy.zeros(3,'i'),
'size': numpy.zeros(3,'d'),
'microstructures': 0,
}
new_header = []
for header in headers:
headitems = map(str.lower,header.split())
if headitems[0] == 'resolution': headitems[0] = 'grid'
if headitems[0] == 'dimension': headitems[0] = 'size'
if headitems[0] in mappings.keys():
if headitems[0] in identifiers.keys():
for i in xrange(len(identifiers[headitems[0]])):
info[headitems[0]][i] = \
mappings[headitems[0]](headitems[headitems.index(identifiers[headitems[0]][i])+1])
else:
info[headitems[0]] = mappings[headitems[0]](headitems[1])
else:
new_header.append(header)
file['croak'].write('grid a b c: %s\n'%(' x '.join(map(str,info['grid']))) + \
'size x y z: %s\n'%(' x '.join(map(str,info['size']))) + \
'origin x y z: %s\n'%(' : '.join(map(str,info['origin']))) + \
'homogenization: %i\n'%info['homogenization'] + \
'microstructures: %i\n\n'%info['microstructures'])
if numpy.any(info['grid'] < 1):
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file['croak'].write('invalid grid a b c.\n')
sys.exit()
if numpy.any(info['size'] <= 0.0):
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file['croak'].write('invalid size x y z.\n')
sys.exit()
newInfo['grid'] = numpy.array([{True:int(o*float(n.translate(None,'xX'))), False: int(n.translate(None,'xX'))}[n[-1].lower() == 'x'] for o,n in zip(info['grid'],options.grid)],'i')
newInfo['size'] = numpy.array([{True: o*float(n.translate(None,'xX')) , False: float(n.translate(None,'xX'))}[n[-1].lower() == 'x'] for o,n in zip(info['size'],options.size)],'d')
newInfo['grid'] = numpy.where(newInfo['grid'] <= 0 , info['grid'],newInfo['grid'])
newInfo['size'] = numpy.where(newInfo['size'] <= 0.0, info['size'],newInfo['size'])
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#--- read data ------------------------------------------------------------------------------------
microstructure = numpy.zeros(info['grid'],'i')
i = 0
for line in content:
items = line.split()
if len(items) > 2:
if items[1].lower() == 'of': items = [int(items[2])]*int(items[0])
elif items[1].lower() == 'to': items = xrange(int(items[0]),1+int(items[2]))
else: items = map(int,items)
else: items = map(int,items)
for item in items:
microstructure[i%info['grid'][0],
(i/info['grid'][0])%info['grid'][1],
i/info['grid'][0] /info['grid'][1]] = item
i += 1
newInfo['microstructures'] = microstructure.max()
formatwidth = 1+int(math.floor(math.log10(microstructure.max())))
if (any(newInfo['grid'] != info['grid'])):
file['croak'].write('--> grid a b c: %s\n'%(' x '.join(map(str,newInfo['grid']))))
if (any(newInfo['size'] != info['size'])):
file['croak'].write('--> size x y z: %s\n'%(' x '.join(map(str,newInfo['size']))))
if (newInfo['microstructures'] != info['microstructures']):
file['croak'].write('--> microstructures: %i\n'%newInfo['microstructures'])
if numpy.any(newInfo['grid'] < 1):
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file['croak'].write('invalid new grid a b c.\n')
sys.exit()
if numpy.any(newInfo['size'] <= 0.0):
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file['croak'].write('invalid new size x y z.\n')
sys.exit()
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#--- assemble header ------------------------------------------------------------------------------
new_header.append('$Id$\n')
new_header.append("grid\ta %i\tb %i\tc %i\n"%(newInfo['grid'][0],newInfo['grid'][1],newInfo['grid'][2]))
new_header.append("size\tx %f\ty %f\tz %f\n"%(newInfo['size'][0],newInfo['size'][1],newInfo['size'][2]))
new_header.append("origin\tx %f\ty %f\tz %f\n"%(info['origin'][0],info['origin'][1],info['origin'][2]))
new_header.append("microstructures\t%i\n"%newInfo['microstructures'])
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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#--- scale microstructure -------------------------------------------------------------------------
for c in xrange(newInfo['grid'][2]):
z = int(info['grid'][2]*(c+0.5)/newInfo['grid'][2])%info['grid'][2]
for b in xrange(newInfo['grid'][1]):
y = int(info['grid'][1]*(b+0.5)/newInfo['grid'][1])%info['grid'][1]
for a in xrange(newInfo['grid'][0]):
x = int(info['grid'][0]*(a+0.5)/newInfo['grid'][0])%info['grid'][0]
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file['output'].write(str(microstructure[x,y,z]).rjust(formatwidth) + {True:' ',False:'\n'}
[options.twoD])
file['output'].write({True:'\n',False:''}[options.twoD])
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#--- output finalization --------------------------------------------------------------------------
if file['name'] != 'STDIN':
file['output'].close()
os.rename(file['name']+'_tmp',file['name'])