#!/usr/bin/env python # -*- coding: UTF-8 no BOM -*- import os,sys,string,re,math,numpy import damask 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 = { 'grid': ['a','b','c'], 'size': ['x','y','z'], 'origin': ['x','y','z'], } mappings = { 'grid': lambda x: int(x), 'size': lambda x: float(x), 'origin': lambda x: float(x), 'homogenization': lambda x: int(x), 'microstructures': 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('-g', '--grid', dest='grid', type='string', nargs = 3, \ help='a,b,c grid of hexahedral box [unchanged]') parser.add_option('-o', '--offset', dest='offset', type='int', nargs = 3, \ help='a,b,c offset from old to new origin of grid %default') parser.add_option('-f', '--fill', dest='fill', type='int', \ help='(background) canvas grain index. "0" selects maximum microstructure index + 1 [%default]') parser.set_defaults(grid = ['0','0','0']) parser.set_defaults(offset = [0,0,0]) 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') theTable = damask.ASCIItable(file['input'],file['output'],labels=False) theTable.head_read() #--- interpret header ---------------------------------------------------------------------------- info = { 'grid': numpy.zeros(3,'i'), 'size': numpy.zeros(3,'d'), 'origin': numpy.zeros(3,'d'), 'microstructures': 0, 'homogenization': 0, } newInfo = { 'grid': numpy.zeros(3,'i'), 'origin': numpy.zeros(3,'d'), 'microstructures': 0, } extra_header = [] for header in theTable.info: headitems = map(str.lower,header.split()) if len(headitems) == 0: continue # skip blank lines if headitems[0] == 'resolution': headitems[0] = 'grid' if headitems[0] == 'dimension': headitems[0] = 'size' 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]) else: extra_header.append(header) file['croak'].write('grid a b c: %s\n'%(' x '.join(map(str,info['grid']))) + \ 'size x y z: %s\n'%(' x '.join(map(str,info['size']))) + \ 'origin x y z: %s\n'%(' : '.join(map(str,info['origin']))) + \ 'homogenization: %i\n'%info['homogenization'] + \ 'microstructures: %i\n'%info['microstructures']) if numpy.any(info['grid'] < 1): file['croak'].write('invalid grid a b c.\n') continue if numpy.any(info['size'] <= 0.0): file['croak'].write('invalid size x y z.\n') continue #--- read data ------------------------------------------------------------------------------------ microstructure = numpy.zeros(info['grid'].prod(),'i') # initialize as flat array i = 0 theTable.data_rewind() while theTable.data_read(): items = theTable.data if len(items) > 2: if items[1].lower() == 'of': items = [int(items[2])]*int(items[0]) elif items[1].lower() == 'to': items = xrange(int(items[0]),1+int(items[2])) else: items = map(int,items) else: items = map(int,items) s = len(items) microstructure[i:i+s] = items i += s #--- do work ------------------------------------------------------------------------------------ newInfo['grid'] = numpy.array([{True:int(o*float(n.translate(None,'xX'))), False: int(n.translate(None,'xX'))}[n[-1].lower() == 'x'] for o,n in zip(info['grid'],options.grid)],'i') newInfo['grid'] = numpy.where(newInfo['grid'] <= 0 , info['grid'],newInfo['grid']) microstructure = microstructure.reshape(info['grid'],order='F') microstructure_cropped = numpy.zeros(newInfo['grid'],'i') microstructure_cropped.fill({True:options.fill,False:microstructure.max()+1}[options.fill>0]) xindex = list(set(xrange(options.offset[0],options.offset[0]+newInfo['grid'][0])) & \ set(xrange(info['grid'][0]))) yindex = list(set(xrange(options.offset[1],options.offset[1]+newInfo['grid'][1])) & \ set(xrange(info['grid'][1]))) zindex = list(set(xrange(options.offset[2],options.offset[2]+newInfo['grid'][2])) & \ set(xrange(info['grid'][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)] newInfo['size'] = info['size']/info['grid']*newInfo['grid'] newInfo['origin'] = info['origin']+info['size']/info['grid']*options.offset newInfo['microstructures'] = microstructure_cropped.max() #--- report --------------------------------------------------------------------------------------- if (any(newInfo['grid'] != info['grid'])): file['croak'].write('--> grid a b c: %s\n'%(' x '.join(map(str,newInfo['grid'])))) if (any(newInfo['size'] != info['size'])): file['croak'].write('--> size x y z: %s\n'%(' x '.join(map(str,newInfo['size'])))) if (any(newInfo['origin'] != info['origin'])): file['croak'].write('--> origin x y z: %s\n'%(' : '.join(map(str,newInfo['size'])))) if (newInfo['microstructures'] != info['microstructures']): file['croak'].write('--> microstructures: %i\n'%newInfo['microstructures']) if numpy.any(newInfo['grid'] < 1): file['croak'].write('invalid new grid a b c.\n') continue if numpy.any(newInfo['size'] <= 0.0): file['croak'].write('invalid new size x y z.\n') continue #--- write header --------------------------------------------------------------------------------- theTable.labels_clear() theTable.info_clear() theTable.info_append(extra_header+[ "$Id$", "grid\ta %i\tb %i\tc %i"%(newInfo['grid'][0],newInfo['grid'][1],newInfo['grid'][2],), "size\tx %f\ty %f\tz %f"%(newInfo['size'][0],newInfo['size'][1],newInfo['size'][2],), "origin\tx %f\ty %f\tz %f"%(newInfo['origin'][0],newInfo['origin'][1],newInfo['origin'][2],), "microstructures\t%i"%(newInfo['microstructures']), "homogenization\t%i"%info['homogenization'], ]) theTable.head_write() theTable.output_flush() # --- write microstructure information ------------------------------------------------------------ formatwidth = int(math.floor(math.log10(microstructure_cropped.max())+1)) theTable.data = microstructure_cropped.reshape((newInfo['grid'][0],newInfo['grid'][1]*newInfo['grid'][2]),order='F').transpose() theTable.data_writeArray('%%%ii'%(formatwidth)) #--- output finalization -------------------------------------------------------------------------- if file['name'] != 'STDIN': file['input'].close() file['output'].close() os.rename(file['name']+'_tmp',file['name'])