DAMASK_EICMD/processing/pre/geom_canvas.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
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#--------------------------------------------------------------------------------------------------
class extendedOption(Option):
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#--------------------------------------------------------------------------------------------------
# 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)
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#--------------------------------------------------------------------------------------------------
# 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),
}
parser = OptionParser(option_class=extendedOption, usage='%prog options [file[s]]', description = """
Changes the (three-dimensional) canvas of a spectral geometry description.
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""" + string.replace('$Id$','\n','\\n')
)
parser.add_option('-g', '--grid', dest='grid', type='int', nargs = 3, \
help='a,b,c grid of hexahedral box [unchanged]')
parser.add_option('-o', '--offset', dest='offset', type='int', nargs = 3, \
help='a,b,c offset from old to new origin of grid %default')
parser.add_option('-f', '--fill', dest='fill', type='int', \
help='(background) canvas grain index. "0" selects maximum microstructure index + 1 [%default]')
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(offset = [0,0,0])
parser.set_defaults(twoD = False)
parser.set_defaults(fill = 0)
(options, filenames) = parser.parse_args()
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#--- 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,
})
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#--- 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,
}
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newInfo = {
'grid': numpy.array(options.grid),
'size': numpy.zeros(3,'d'),
'origin': 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])
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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'%info['microstructures'])
if numpy.any(info['grid'] < 1):
file['croak'].write('invalid grid a b c.\n')
sys.exit()
if numpy.any(info['size'] <= 0.0):
file['croak'].write('invalid size x y z.\n')
sys.exit()
#--- read data ------------------------------------------------------------------------------------
microstructure = numpy.zeros(info['grid'],'i')
i = 0
for line in content:
for item in map(int,line.split()):
microstructure[i%info['grid'][0],
(i/info['grid'][0])%info['grid'][1],
i/info['grid'][0] /info['grid'][1]] = item
i += 1
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microstructure_cropped = numpy.zeros(options.grid,'i')
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microstructure_cropped.fill({True:options.fill,False:microstructure.max()+1}[options.fill>0])
xindex = list(set(xrange(options.offset[0],options.offset[0]+options.grid[0])) & \
set(xrange(info['grid'][0])))
yindex = list(set(xrange(options.offset[1],options.offset[1]+options.grid[1])) & \
set(xrange(info['grid'][1])))
zindex = list(set(xrange(options.offset[2],options.offset[2]+options.grid[2])) & \
set(xrange(info['grid'][2])))
translate_x = [i - options.offset[0] for i in xindex]
translate_y = [i - options.offset[1] for i in yindex]
translate_z = [i - options.offset[2] for i in zindex]
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)]
formatwidth = int(math.floor(math.log10(microstructure.max())+1))
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if numpy.all(options.grid == 0):
newInfo['grid'] = info['grid']
newInfo['microstructures'] = microstructure_cropped.max()
newInfo['size'] = info['size']/info['grid']*options.grid
newInfo['origin'] = info['origin']+info['size']/info['grid']*options.offset
#--- report ---------------------------------------------------------------------------------------
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 (any(newInfo['origin'] != info['origin'])):
file['croak'].write('--> origin x y z: %s\n'%(' : '.join(map(str,newInfo['size']))))
if (newInfo['microstructures'] != info['microstructures']):
file['croak'].write('--> microstructures: %i\n'%newInfo['microstructures'])
if numpy.any(newInfo['grid'] < 1):
file['croak'].write('invalid new grid a b c.\n')
sys.exit()
if numpy.any(newInfo['size'] <= 0.0):
file['croak'].write('invalid new size x y z.\n')
sys.exit()
# --- 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"%(
newInfo['origin'][0],newInfo['origin'][1],newInfo['origin'][2]))
new_header.append("homogenization\t%i\n"%info['homogenization'])
new_header.append("microstructures\t%i\n"%newInfo['microstructures'])
file['output'].write('%i\theader\n'%(len(new_header))+''.join(new_header))
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# --- write microstructure information ------------------------------------------------------------
for z in xrange(options.grid[2]):
for y in xrange(options.grid[1]):
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file['output'].write({True:' ',False:'\n'}[options.twoD].join(map(lambda x: \
('%%%ii'%formatwidth)%x, microstructure_cropped[:,y,z])) + '\n')
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#--- output finalization --------------------------------------------------------------------------
if file['name'] != 'STDIN':
file['output'].close()
os.rename(file['name']+'_tmp',file['name'])