162 lines
6.7 KiB
Python
Executable File
162 lines
6.7 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'],
|
|
}
|
|
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'])
|
|
|