DAMASK_EICMD/processing/pre/spectral_geomCanvas.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 = {
'resolution': ['a','b','c'],
'dimension': ['x','y','z'],
}
mappings = {
'resolution': lambda x: int(x),
'dimension': lambda x: float(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: spectral_geomCrop.py 1449 2012-04-24 11:31:18Z MPIE\t.elachkar $','\n','\\n')
)
parser.add_option('-b', '--box', dest='resolution', type='int', nargs = 3, \
help='resolution of new canvas (a,b,c)')
parser.add_option('-o', '--offset', dest='offset', type='int', nargs = 3, \
help='offset from old to new origin of grid')
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})
else:
for name in filenames:
if os.path.exists(name):
files.append({'name':name, 'input':open(name), 'output':open(name+'_tmp','w')})
# ------------------------------------------ loop over input files ---------------------------------------
for file in files:
if file['name'] != 'STDIN': print file['name']
# 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()
if 0 in options.resolution:
for header in headers:
headitems = header.split()
if headitems[0] == 'resolution': # located resolution entry
for i in xrange(3):
options.resolution[i] = mappings['resolution'](headitems[headitems.index(identifiers['resolution'][i])+1])
resolution = [0,0,0]
dimension = [0.0,0.0,0.0]
new_header = []
for header in headers:
headitems = header.split()
if headitems[0] == 'resolution': # located resolution entry
for i in xrange(3):
resolution[i] = mappings['resolution'](headitems[headitems.index(identifiers['resolution'][i])+1])
header = "resolution\ta %i\tb %i\tc %i\n"%(options.resolution[0],options.resolution[1],options.resolution[2],)
if headitems[0] == 'dimension': # located dimension entry
for i in xrange(3):
dimension[i] = mappings['dimension'](headitems[headitems.index(identifiers['dimension'][i])+1])
header = "dimension\tx %f\ty %f\tz %f\n"%(dimension[0]/resolution[0]*options.resolution[0],
dimension[1]/resolution[1]*options.resolution[1],
dimension[2]/resolution[2]*options.resolution[2],)
new_header.append(header)
if resolution == [0,0,0]:
print 'no resolution info found.'
sys.exit(1)
if dimension == [0.0,0.0,0.0]:
print 'no dimension info found.'
sys.exit(1)
if file['name'] != 'STDIN':
print 'resolution: %s'%(' x '.join(map(str,resolution)))
print 'dimension: %s'%(' x '.join(map(str,dimension)))
microstructure = numpy.zeros(resolution,'i')
i = 0
for line in content:
for item in map(int,line.split()):
microstructure[i%resolution[0],(i/resolution[0])%resolution[1],i/resolution[0]/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(resolution[0])))
yindex = list(set(xrange(options.offset[1],options.offset[1]+options.resolution[1])) & set(xrange(resolution[1])))
zindex = list(set(xrange(options.offset[2],options.offset[2]+options.resolution[2])) & set(xrange(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 = ''.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'])