DAMASK_EICMD/processing/pre/geom_canvas.py

186 lines
7.5 KiB
Python
Executable File

#!/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 = {
'resolution': ['a','b','c'],
'dimension': ['x','y','z'],
'origin': ['x','y','z'],
}
mappings = {
'resolution': lambda x: int(x),
'dimension': 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.
""" + string.replace('$Id$','\n','\\n')
)
parser.add_option('-b', '--box', dest='resolution', type='int', nargs = 3, \
help='resolution of new canvas (a,b,c) %default')
parser.add_option('-o', '--offset', dest='offset', type='int', nargs = 3, \
help='offset from old to new origin of grid %default')
parser.add_option('-f', '--fill', dest='fill', type='int', \
help='(background) canvas grain index')
parser.add_option('-2', '--twodimensional', dest='twoD', action='store_true', \
help='output geom file with two-dimensional data arrangement')
parser.set_defaults(resolution = [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()
# ------------------------------------------ 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')
# get labels by either read the first row, or - if keyword header is present - the last line of the header
firstline = file['input'].readline()
m = re.search('(\d+)\s*head', firstline.lower())
if m:
headerlines = int(m.group(1))
headers = [firstline]+[file['input'].readline() for i in range(headerlines)]
else:
headerlines = 1
headers = firstline
content = file['input'].readlines()
file['input'].close()
info = {'resolution': numpy.array(options.resolution),
'dimension': numpy.array([0.0,0.0,0.0]),
'origin': numpy.array([0.0,0.0,0.0]),
'homogenization': 1,
}
new_header = []
for header in headers:
headitems = map(str.lower,header.split())
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])
if options.resolution == [0,0,0]:
options.resolution = info['resolution']
if info['resolution'].all() == 0:
file['croak'].write('no resolution info found.\n')
continue
if info['dimension'] == [0.0,0.0,0.0]:
file['croak'].write('no dimension info found.\n')
continue
file['croak'].write('resolution: %s\n'%(' x '.join(map(str,info['resolution']))) + \
'dimension: %s\n'%(' x '.join(map(str,info['dimension']))) + \
'origin: %s\n'%(' : '.join(map(str,info['origin']))) + \
'homogenization: %i\n'%info['homogenization'])
new_header.append("resolution\ta %i\tb %i\tc %i\n"%(
options.resolution[0],
options.resolution[1],
options.resolution[2],))
new_header.append("dimension\tx %f\ty %f\tz %f\n"%(
info['dimension'][0]/info['resolution'][0]*options.resolution[0],
info['dimension'][1]/info['resolution'][1]*options.resolution[1],
info['dimension'][2]/info['resolution'][2]*options.resolution[2],))
new_header.append("origin\tx %f\ty %f\tz %f\n"%(
info['origin'][0]+info['dimension'][0]/info['resolution'][0]*options.offset[0],
info['origin'][1]+info['dimension'][1]/info['resolution'][1]*options.offset[1],
info['origin'][2]+info['dimension'][2]/info['resolution'][2]*options.offset[2],))
new_header.append("homogenization\t%i\n"%info['homogenization'])
microstructure = numpy.zeros(info['resolution'],'i')
i = 0
for line in content:
for item in map(int,line.split()):
microstructure[i%info['resolution'][0],
(i/info['resolution'][0])%info['resolution'][1],
i/info['resolution'][0] /info['resolution'][1]] = item
i += 1
microstructure_cropped = numpy.zeros(options.resolution,'i')
microstructure_cropped.fill({True:options.fill,False:microstructure.max()+1}[options.fill>0])
xindex = list(set(xrange(options.offset[0],options.offset[0]+options.resolution[0])) & set(xrange(info['resolution'][0])))
yindex = list(set(xrange(options.offset[1],options.offset[1]+options.resolution[1])) & set(xrange(info['resolution'][1])))
zindex = list(set(xrange(options.offset[2],options.offset[2]+options.resolution[2])) & set(xrange(info['resolution'][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))
# ------------------------------------------ assemble header ---------------------------------------
output = '%i\theader\n'%(len(new_header))
output += ''.join(new_header)
# ------------------------------------- regenerate texture information ----------------------------------
for z in xrange(options.resolution[2]):
for y in xrange(options.resolution[1]):
output += {True:' ',False:'\n'}[options.twoD].join(map(lambda x: ('%%%ii'%formatwidth)%x, microstructure_cropped[:,y,z])) + '\n'
#output += '\n'
# ------------------------------------------ output result ---------------------------------------
file['output'].write(output)
if file['name'] != 'STDIN':
file['output'].close()
os.rename(file['name']+'_tmp',file['name'])