#!/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 scriptID = '$Id: geom_addPrimitive.py 3412 2014-08-22 16:58:53Z MPIE\m.diehl $' scriptName = scriptID.split()[1] oversampling = 2. #-------------------------------------------------------------------------------------------------- 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 #-------------------------------------------------------------------------------------------------- synonyms = { 'grid': ['resolution'], 'size': ['dimension'], } 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 = """ Positions a geometric object within the (three-dimensional) canvas of a spectral geometry description. Depending on the sign of the dimension parameters, these objects can be boxes, cylinders, or ellipsoids. """ + string.replace(scriptID,'\n','\\n') ) parser.add_option('-o', '--origin', '-c', '--center', dest='center', type='int', nargs = 3, metavar=' '.join(['int']*3), help='a,b,c origin of primitive %default') parser.add_option('-d', '--dimension', dest='dimension', type='int', nargs = 3, metavar=' '.join(['int']*3), help='a,b,c extension of hexahedral box; negative values are diameters') parser.add_option('-f', '--fill', dest='fill', type='int', metavar = 'int', help='grain index to fill primitive. "0" selects maximum microstructure index + 1 [%default]') parser.add_option('-q', '--quaternion', dest='quaternion', type='float', nargs = 4, metavar=' '.join(['float']*4), help = 'rotation of primitive as quaternion') parser.add_option('-a', '--angleaxis', dest='angleaxis', nargs = 4, metavar=' '.join(['float']*4), help = 'rotation of primitive as angle and axis') parser.add_option( '--degrees', dest='degrees', action='store_true', help = 'angle is given in degrees [%default]') parser.set_defaults(center = [0,0,0], fill = 0, quaternion = [], angleaxis = [], degrees = False, ) (options, filenames) = parser.parse_args() if options.angleaxis != []: options.angleaxis = map(float,options.angleaxis) rotation = damask.Quaternion().fromAngleAxis(numpy.radians(options.angleaxis[0]) if options.degrees else options.angleaxis[0], options.angleaxis[1:4]).conjugated() elif options.quaternion != []: options.rotation = map(float,options.rotation) rotation = damask.Quaternion(options.quaternion).conjugated() else: rotation = damask.Quaternion().conjugated() options.center = numpy.array(options.center) invRotation = rotation.conjugated() # rotation of gridpos into primitive coordinate system #--- 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('\033[1m'+scriptName+'\033[0m: '+file['name']+'\n') else: file['croak'].write('\033[1m'+scriptName+'\033[0m\n') table = damask.ASCIItable(file['input'],file['output'],labels = False) table.head_read() #--- interpret header ---------------------------------------------------------------------------- info = { 'grid': numpy.zeros(3,'i'), 'size': numpy.zeros(3,'d'), 'origin': numpy.zeros(3,'d'), 'homogenization': 0, 'microstructures': 0, } newInfo = { 'grid': numpy.zeros(3,'i'), 'origin': numpy.zeros(3,'d'), 'microstructures': 0, } extra_header = [] for header in table.info: headitems = map(str.lower,header.split()) if len(headitems) == 0: continue # skip blank lines for synonym,alternatives in synonyms.iteritems(): if headitems[0] in alternatives: headitems[0] = synonym 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 while table.data_read(): items = table.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 ------------------------------------------------------------------------------------ if options.fill == 0: options.fill = microstructure.max()+1 microstructure = microstructure.reshape(info['grid'],order='F') if options.dimension != None: mask = (numpy.array(options.dimension) < 0).astype(float) # zero where positive dimension, otherwise one dim = abs(numpy.array(options.dimension)) # dimensions of primitive body pos = numpy.zeros(3,dtype='float') # hiresPrimitive = numpy.zeros((2*dim[0],2*dim[1],2*dim[2],3)) # primitive discretized at twice the grid resolution for i,pos[0] in enumerate(numpy.arange(-dim[0]/oversampling,(dim[0]+1)/oversampling,1./oversampling)): for j,pos[1] in enumerate(numpy.arange(-dim[1]/oversampling,(dim[1]+1)/oversampling,1./oversampling)): for k,pos[2] in enumerate(numpy.arange(-dim[2]/oversampling,(dim[2]+1)/oversampling,1./oversampling)): gridpos = numpy.floor(rotation*pos) # rotate and lock into spacial grid primPos = invRotation*gridpos # rotate back to primitive coordinate system if numpy.dot(mask*primPos/dim,mask*primPos/dim) <= 0.25 and \ numpy.all(abs((1.-mask)*primPos/dim) <= 0.5): # inside ellipsoid and inside box microstructure[(gridpos[0]+options.center[0])%info['grid'][0], (gridpos[1]+options.center[1])%info['grid'][1], (gridpos[2]+options.center[2])%info['grid'][2]] = options.fill # assign microstructure index newInfo['microstructures'] = microstructure.max() #--- report --------------------------------------------------------------------------------------- if (newInfo['microstructures'] != info['microstructures']): file['croak'].write('--> microstructures: %i\n'%newInfo['microstructures']) #--- write header --------------------------------------------------------------------------------- table.labels_clear() table.info_clear() table.info_append(extra_header+[ scriptID + ' ' + ' '.join(sys.argv[1:]), "grid\ta %i\tb %i\tc %i"%(info['grid'][0],info['grid'][1],info['grid'][2],), "size\tx %f\ty %f\tz %f"%(info['size'][0],info['size'][1],info['size'][2],), "origin\tx %f\ty %f\tz %f"%(info['origin'][0],info['origin'][1],info['origin'][2],), "homogenization\t%i"%info['homogenization'], "microstructures\t%i"%(newInfo['microstructures']), ]) table.head_write() table.output_flush() # --- write microstructure information ------------------------------------------------------------ formatwidth = int(math.floor(math.log10(microstructure.max())+1)) table.data = microstructure.reshape((info['grid'][0],info['grid'][1]*info['grid'][2]),order='F').transpose() table.data_writeArray('%%%ii'%(formatwidth),delimiter=' ') #--- output finalization -------------------------------------------------------------------------- if file['name'] != 'STDIN': table.input_close() table.output_close() os.rename(file['name']+'_tmp',file['name'])