still improving preprocessing scripts
This commit is contained in:
Martin Diehl
parent
190a59b707
commit
17b81fda7c
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@ -4,10 +4,9 @@
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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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#--------------------------------------------------------------------------------------------------
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class extendedOption(Option):
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# -----------------------------
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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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@ -24,8 +23,9 @@ class extendedOption(Option):
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Option.take_action(self, action, dest, opt, value, values, parser)
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# ----------------------- MAIN -------------------------------
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#--------------------------------------------------------------------------------------------------
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# MAIN
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#--------------------------------------------------------------------------------------------------
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identifiers = {
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'grid': ['a','b','c'],
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'size': ['x','y','z'],
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@ -38,7 +38,6 @@ mappings = {
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'homogenization': lambda x: int(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('$Id$','\n','\\n')
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@ -60,7 +59,7 @@ 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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#--- setup file handles --------------------------------------------------------------------------
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files = []
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if filenames == []:
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files.append({'name':'STDIN',
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@ -77,13 +76,10 @@ else:
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'croak':sys.stdout,
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})
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# ------------------------------------------ loop over input files ---------------------------------------
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#--- loop over input files ------------------------------------------------------------------------
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for file in files:
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if file['name'] != 'STDIN': file['croak'].write(file['name']+'\n')
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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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@ -96,13 +92,20 @@ for file in files:
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content = file['input'].readlines()
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file['input'].close()
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#--- interprete header ----------------------------------------------------------------------------
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info = {
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'grid': numpy.array(options.grid),
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'size': numpy.array([0.0,0.0,0.0]),
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'origin': numpy.array([0.0,0.0,0.0]),
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'grid': numpy.zeros(3,'i'),
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'size': numpy.zeros(3,'d'),
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'origin': numpy.zeros(3,'d'),
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'microstructures': 0,
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'homogenization': 0,
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}
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newInfo = {
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'grid': numpy.array(options.grid),
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'size': numpy.zeros(3,'d'),
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'origin': numpy.zeros(3,'d'),
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'microstructures': 0,
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}
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new_header = []
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for header in headers:
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@ -117,15 +120,20 @@ for file in files:
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else:
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info[headitems[0]] = mappings[headitems[0]](headitems[1])
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if numpy.all(options.grid == 0):
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options.grid = info['grid']
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if numpy.all(info['grid'] == 0):
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file['croak'].write('no grid info found.\n')
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continue
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if numpy.all(info['size'] == 0.0):
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file['croak'].write('no size info found.\n')
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continue
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file['croak'].write('grid a b c: %s\n'%(' x '.join(map(str,info['grid']))) + \
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'size x y z: %s\n'%(' x '.join(map(str,info['size']))) + \
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'origin x y z: %s\n'%(' : '.join(map(str,info['origin']))) + \
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'homogenization: %i\n'%info['homogenization'] + \
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'microstructures: %i\n'%info['microstructures'])
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if numpy.any(info['grid'] < 1):
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file['croak'].write('invalid grid a b c.\n')
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sys.exit()
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if numpy.any(info['size'] <= 0.0):
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file['croak'].write('invalid size x y z.\n')
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sys.exit()
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#--- read data ------------------------------------------------------------------------------------
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microstructure = numpy.zeros(info['grid'],'i')
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i = 0
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for line in content:
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@ -134,26 +142,9 @@ for file in files:
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(i/info['grid'][0])%info['grid'][1],
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i/info['grid'][0] /info['grid'][1]] = item
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i += 1
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file['croak'].write('-- input --\n' + \
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'grid a b c: %s\n'%(' x '.join(map(str,info['grid']))) + \
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'size x y z: %s\n'%(' x '.join(map(str,info['size']))) + \
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'origin x y z: %s\n'%(' : '.join(map(str,info['origin']))) + \
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'homogenization: %i\n'%info['homogenization'] + \
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'microstructures: %i\n'%info['microstructures'])
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info['microstructures'] = microstructure.max()
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newSize = info['size']/info['grid']*options.grid
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newOrigin = info['origin']+info['size']/info['grid']*options.offset
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new_header.append("grid\ta %i\tb %i\tc %i\n"%(options.grid[0],options.grid[1],options.grid[2]))
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new_header.append("size\tx %f\ty %f\tz %f\n"%(newSize[0],newSize[1],newSize[2]))
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new_header.append("origin\tx %f\ty %f\tz %f\n"%(newOrigin[0],newOrigin[1],newOrigin[2]))
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new_header.append("homogenization\t%i\n"%info['homogenization'])
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new_header.append("microstructures\t%i\n"%info['microstructures'])
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microstructure_cropped = numpy.zeros(options.grid,'i')
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microstructure_cropped.fill({True:options.fill,False:info['microstructures']+1}[options.fill>0])
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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.grid[0])) & \
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set(xrange(info['grid'][0])))
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yindex = list(set(xrange(options.offset[1],options.offset[1]+options.grid[1])) & \
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@ -171,28 +162,49 @@ for file in files:
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min(zindex):(max(zindex)+1)]
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formatwidth = int(math.floor(math.log10(microstructure.max())+1))
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file['croak'].write('-- output --\n' +\
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'grid a b c: %s\n'%(' x '.join(map(str,options.grid))) + \
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'size x y z: %s\n'%(' x '.join(map(str,newSize))) + \
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'origin x y z: %s\n'%(' x '.join(map(str,newOrigin))) + \
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'microstructures: %i\n'%microstructure.max())
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# ------------------------------------------ assemble header ---------------------------------------
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if numpy.all(options.grid == 0):
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newInfo['grid'] = info['grid']
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newInfo['microstructures'] = microstructure_cropped.max()
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newInfo['size'] = info['size']/info['grid']*options.grid
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newInfo['origin'] = info['origin']+info['size']/info['grid']*options.offset
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output = '%i\theader\n'%(len(new_header))
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output += ''.join(new_header)
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# ------------------------------------- regenerate texture information ----------------------------
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#--- report ---------------------------------------------------------------------------------------
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if (any(newInfo['grid'] != info['grid'])):
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file['croak'].write('--> grid a b c: %s\n'%(' x '.join(map(str,newInfo['grid']))))
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if (any(newInfo['size'] != info['size'])):
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file['croak'].write('--> size x y z: %s\n'%(' x '.join(map(str,newInfo['size']))))
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if (any(newInfo['origin'] != info['origin'])):
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file['croak'].write('--> origin x y z: %s\n'%(' : '.join(map(str,newInfo['size']))))
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if (newInfo['microstructures'] != info['microstructures']):
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file['croak'].write('--> microstructures: %i\n'%newInfo['microstructures'])
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if numpy.any(newInfo['grid'] < 1):
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file['croak'].write('invalid new grid a b c.\n')
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sys.exit()
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if numpy.any(newInfo['size'] <= 0.0):
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file['croak'].write('invalid new size x y z.\n')
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sys.exit()
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# --- assemble header -----------------------------------------------------------------------------
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new_header.append('$Id$\n')
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new_header.append("grid\ta %i\tb %i\tc %i\n"%(
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newInfo['grid'][0],newInfo['grid'][1],newInfo['grid'][2]))
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new_header.append("size\tx %f\ty %f\tz %f\n"%(
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newInfo['size'][0],newInfo['size'][1],newInfo['size'][2]))
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new_header.append("origin\tx %f\ty %f\tz %f\n"%(
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newInfo['origin'][0],newInfo['origin'][1],newInfo['origin'][2]))
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new_header.append("homogenization\t%i\n"%info['homogenization'])
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new_header.append("microstructures\t%i\n"%newInfo['microstructures'])
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file['output'].write('%i\theader\n'%(len(new_header))+''.join(new_header))
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# --- write microstructure information ------------------------------------------------------------
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for z in xrange(options.grid[2]):
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for y in xrange(options.grid[1]):
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output += {True:' ',False:'\n'}[options.twoD].join(map(lambda x: \
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('%%%ii'%formatwidth)%x, microstructure_cropped[:,y,z])) + '\n'
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# ------------------------------------------ output result ---------------------------------------
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file['output'].write(output)
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file['output'].write({True:' ',False:'\n'}[options.twoD].join(map(lambda x: \
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('%%%ii'%formatwidth)%x, microstructure_cropped[:,y,z])) + '\n')
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#--- output finalization --------------------------------------------------------------------------
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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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@ -211,7 +211,6 @@ for file in files:
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False:'\n'}[options.twoD].\
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join(map(lambda x: str(x).rjust(formatwidth),\
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indices[n*info['grid'][0]:(n+1)*info['grid'][0]]))+'\n')
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#--- output finalization --------------------------------------------------------------------------
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if file['name'] != 'STDIN':
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@ -126,15 +126,15 @@ for file in files:
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'microstructures: %i\n\n'%info['microstructures'])
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if numpy.any(info['grid'] < 1):
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file['croak'].write('no valid grid info found.\n')
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file['croak'].write('invalid grid a b c.\n')
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sys.exit()
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if numpy.any(info['size'] <= 0.0):
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file['croak'].write('no valid size info found.\n')
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file['croak'].write('invalid size x y z.\n')
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sys.exit()
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if numpy.all(info['grid'] == 0):
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newInfo['grid'] = info['grid']
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if numpy.all(info['size'] == 0.0)::
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if numpy.all(info['size'] == 0.0):
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newInfo['size'] = info['size']
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#--- read data ------------------------------------------------------------------------------------
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@ -157,10 +157,10 @@ for file in files:
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file['croak'].write('--> microstructures: %i\n'%newInfo['microstructures'])
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if numpy.any(newInfo['grid'] < 1):
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file['croak'].write('no valid new grid info found.\n')
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file['croak'].write('invalid new grid a b c.\n')
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sys.exit()
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if numpy.any(newInfo['size'] <= 0.0):
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file['croak'].write('no valid new size info found.\n')
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file['croak'].write('invalid new size x y z.\n')
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sys.exit()
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#--- assemble header ------------------------------------------------------------------------------
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@ -170,8 +170,7 @@ for file in files:
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new_header.append("origin\tx %f\ty %f\tz %f\n"%(info['origin'][0],info['origin'][1],info['origin'][2]))
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new_header.append("microstructures\t%i\n"%newInfo['microstructures'])
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new_header.append("homogenization\t%i\n"%info['homogenization'])
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output = '%i\theader\n'%(len(new_header))
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output += ''.join(new_header)
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file['output'].write('%i\theader\n'%(len(new_header))+''.join(new_header))
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#--- scale microstructure -------------------------------------------------------------------------
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for c in xrange(newInfo['grid'][2]):
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@ -180,9 +179,9 @@ for file in files:
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y = int(info['grid'][1]*(b+0.5)/newInfo['grid'][1])%info['grid'][1]
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for a in xrange(newInfo['grid'][0]):
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x = int(info['grid'][0]*(a+0.5)/newInfo['grid'][0])%info['grid'][0]
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output += str(microstructure[x,y,z]).rjust(formatwidth) + {True:' ',False:'\n'}[options.twoD]
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output += {True:'\n',False:''}[options.twoD]
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file['output'].write(output)
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file['output'].write(str(microstructure[x,y,z]).rjust(formatwidth) + {True:' ',False:'\n'}
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[options.twoD])
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file['output'].write({True:'\n',False:''}[options.twoD])
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#--- output finalization --------------------------------------------------------------------------
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if file['name'] != 'STDIN':
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@ -130,14 +130,14 @@ for file in files:
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'microstructures: %i\n\n'%info['microstructures'])
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if numpy.any(info['grid'] < 1):
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file['croak'].write('no valid grid info found.\n')
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file['croak'].write('invalid grid a b c.\n')
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sys.exit()
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if numpy.any(info['size'] <= 0.0):
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file['croak'].write('no valid size info found.\n')
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file['croak'].write('invalid size x y z.\n')
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sys.exit()
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#--- process input --------------------------------------------------------------------------------
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N = info['grid'][0]*info['grid'][1]*info['grid'][2]
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N = info['grid'].prod()
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microstructure = numpy.zeros(N,'i')
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i = 0
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