script to changes the (three-dimensional) canvas of a spectral geometry description
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Pratheek Shanthraj
parent
dad74ef355
commit
77ee33ec1f
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#!/usr/bin/env python
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# -*- coding: UTF-8 no BOM -*-
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import os,sys,string,re,math,numpy
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from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
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# -----------------------------
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class extendedOption(Option):
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# -----------------------------
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# used for definition of new option parser action 'extend', which enables to take multiple option arguments
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# taken from online tutorial http://docs.python.org/library/optparse.html
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ACTIONS = Option.ACTIONS + ("extend",)
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STORE_ACTIONS = Option.STORE_ACTIONS + ("extend",)
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TYPED_ACTIONS = Option.TYPED_ACTIONS + ("extend",)
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ALWAYS_TYPED_ACTIONS = Option.ALWAYS_TYPED_ACTIONS + ("extend",)
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def take_action(self, action, dest, opt, value, values, parser):
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if action == "extend":
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lvalue = value.split(",")
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values.ensure_value(dest, []).extend(lvalue)
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else:
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Option.take_action(self, action, dest, opt, value, values, parser)
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# ----------------------- MAIN -------------------------------
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identifiers = {
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'resolution': ['a','b','c'],
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'dimension': ['x','y','z'],
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}
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mappings = {
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'resolution': lambda x: int(x),
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'dimension': lambda x: float(x),
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}
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parser = OptionParser(option_class=extendedOption, usage='%prog options [file[s]]', description = """
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Changes the (three-dimensional) canvas of a spectral geometry description.
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""" + string.replace('$Id: spectral_geomCrop.py 1449 2012-04-24 11:31:18Z MPIE\t.elachkar $','\n','\\n')
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)
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parser.add_option('-b', '--box', dest='resolution', type='int', nargs = 3, \
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help='resolution of new canvas (a,b,c)')
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parser.add_option('-o', '--offset', dest='offset', type='int', nargs = 3, \
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help='offset from old to new origin of grid')
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parser.add_option('-f', '--fill', dest='fill', type='int', \
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help='(background) canvas grain index')
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parser.add_option('-2', '--twodimensional', dest='twoD', action='store_true', \
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help='output geom file with two-dimensional data arrangement')
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parser.set_defaults(resolution = [0,0,0])
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parser.set_defaults(offset = [0,0,0])
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parser.set_defaults(twoD = False)
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parser.set_defaults(fill = 0)
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(options, filenames) = parser.parse_args()
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# ------------------------------------------ setup file handles ---------------------------------------
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files = []
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if filenames == []:
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files.append({'name':'STDIN', 'input':sys.stdin, 'output':sys.stdout})
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else:
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for name in filenames:
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if os.path.exists(name):
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files.append({'name':name, 'input':open(name), 'output':open(name+'_tmp','w')})
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# ------------------------------------------ loop over input files ---------------------------------------
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for file in files:
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if file['name'] != 'STDIN': print file['name']
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# get labels by either read the first row, or - if keyword header is present - the last line of the header
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firstline = file['input'].readline()
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m = re.search('(\d+)\s*head', firstline.lower())
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if m:
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headerlines = int(m.group(1))
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headers = [firstline]+[file['input'].readline() for i in range(headerlines)]
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else:
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headerlines = 1
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headers = firstline
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content = file['input'].readlines()
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file['input'].close()
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if 0 in options.resolution:
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for header in headers:
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headitems = header.split()
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if headitems[0] == 'resolution': # located resolution entry
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for i in xrange(3):
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options.resolution[i] = mappings['resolution'](headitems[headitems.index(identifiers['resolution'][i])+1])
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resolution = [0,0,0]
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dimension = [0.0,0.0,0.0]
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new_header = []
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for header in headers:
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headitems = header.split()
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if headitems[0] == 'resolution': # located resolution entry
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for i in xrange(3):
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resolution[i] = mappings['resolution'](headitems[headitems.index(identifiers['resolution'][i])+1])
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header = "resolution\ta %i\tb %i\tc %i\n"%(options.resolution[0],options.resolution[1],options.resolution[2],)
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if headitems[0] == 'dimension': # located dimension entry
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for i in xrange(3):
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dimension[i] = mappings['dimension'](headitems[headitems.index(identifiers['dimension'][i])+1])
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header = "dimension\tx %f\ty %f\tz %f\n"%(dimension[0]/resolution[0]*options.resolution[0],
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dimension[1]/resolution[1]*options.resolution[1],
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dimension[2]/resolution[2]*options.resolution[2],)
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new_header.append(header)
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if resolution == [0,0,0]:
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print 'no resolution info found.'
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sys.exit(1)
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if dimension == [0.0,0.0,0.0]:
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print 'no dimension info found.'
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sys.exit(1)
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if file['name'] != 'STDIN':
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print 'resolution: %s'%(' x '.join(map(str,resolution)))
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print 'dimension: %s'%(' x '.join(map(str,dimension)))
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microstructure = numpy.zeros(resolution,'i')
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i = 0
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for line in content:
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for item in map(int,line.split()):
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microstructure[i%resolution[0],(i/resolution[0])%resolution[1],i/resolution[0]/resolution[1]] = item
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i += 1
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microstructure_cropped = numpy.zeros(options.resolution,'i')
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microstructure_cropped.fill({True:options.fill,False:microstructure.max()+1}[options.fill>0])
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xindex = list(set(xrange(options.offset[0],options.offset[0]+options.resolution[0])) & set(xrange(resolution[0])))
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yindex = list(set(xrange(options.offset[1],options.offset[1]+options.resolution[1])) & set(xrange(resolution[1])))
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zindex = list(set(xrange(options.offset[2],options.offset[2]+options.resolution[2])) & set(xrange(resolution[2])))
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translate_x = [i - options.offset[0] for i in xindex]
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translate_y = [i - options.offset[1] for i in yindex]
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translate_z = [i - options.offset[2] for i in zindex]
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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)]
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formatwidth = int(math.floor(math.log10(microstructure.max()+1)))
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# ------------------------------------------ assemble header ---------------------------------------
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output = ''.join(new_header)
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# ------------------------------------- regenerate texture information ----------------------------------
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for z in xrange(options.resolution[2]):
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for y in xrange(options.resolution[1]):
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output += {True:' ',False:'\n'}[options.twoD].join(map(lambda x: ('%%%ii'%formatwidth)%x, microstructure_cropped[:,y,z])) + '\n'
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#output += '\n'
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# ------------------------------------------ output result ---------------------------------------
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file['output'].write(output)
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if file['name'] != 'STDIN':
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file['output'].close()
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os.rename(file['name']+'_tmp',file['name'])
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@ -83,6 +83,7 @@ bin_link = { \
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'spectral_geomCheck.py',
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'spectral_geomMultiply.py',
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'spectral_geomCrop.py',
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'spectral_geomCanvas.py',
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'spectral_minimalSurface.py',
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'spectral_vicinityOffset.py',
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'spectral_ang2geom.py',
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