diff --git a/processing/pre/geom_rescale.py b/processing/pre/geom_rescale.py index f8cc9311b..e73ab26ea 100755 --- a/processing/pre/geom_rescale.py +++ b/processing/pre/geom_rescale.py @@ -2,6 +2,7 @@ # -*- coding: UTF-8 no BOM -*- import os,sys,string,re,math,numpy +import damask from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP #-------------------------------------------------------------------------------------------------- @@ -26,6 +27,10 @@ class extendedOption(Option): #-------------------------------------------------------------------------------------------------- # MAIN #-------------------------------------------------------------------------------------------------- +synonyms = { + 'grid': ['resolution'], + 'size': ['dimension'], + } identifiers = { 'grid': ['a','b','c'], 'size': ['x','y','z'], @@ -41,6 +46,7 @@ mappings = { parser = OptionParser(option_class=extendedOption, usage='%prog options [file[s]]', description = """ Scales a geometry description independently in x, y, and z direction in terms of grid and/or size. +Either absolute values or relative factors (like "0.25x") can be used. """ + string.replace('$Id$','\n','\\n') ) @@ -48,12 +54,9 @@ parser.add_option('-g', '--grid', dest='grid', type='string', nargs = 3, \ help='a,b,c grid of hexahedral box [unchanged]') parser.add_option('-s', '--size', dest='size', type='string', nargs = 3, \ help='x,y,z size of hexahedral box [unchanged]') -parser.add_option('-2', '--twodimensional', dest='twoD', action='store_true', \ - help='output geom file with two-dimensional data arrangement [%default]') parser.set_defaults(grid = ['0','0','0']) parser.set_defaults(size = ['0.0','0.0','0.0']) -parser.set_defaults(twoD = False) (options, filenames) = parser.parse_args() @@ -78,37 +81,29 @@ else: for file in files: if file['name'] != 'STDIN': file['croak'].write(file['name']+'\n') - firstline = file['input'].readline() - m = re.search('(\d+)\s*head', firstline.lower()) - if m: - headerlines = int(m.group(1)) - headers = [file['input'].readline() for i in range(headerlines)] - else: - headerlines = 1 - headers = firstline + theTable = damask.ASCIItable(file['input'],file['output'],labels=False) + theTable.head_read() - content = file['input'].readlines() - file['input'].close() - -#--- interprete header ---------------------------------------------------------------------------- +#--- interpret header ---------------------------------------------------------------------------- info = { - 'grid': numpy.zeros(3,'i'), - 'size': numpy.zeros(3,'d'), - 'origin': numpy.zeros(3,'d'), + 'grid': numpy.zeros(3,'i'), + 'size': numpy.zeros(3,'d'), + 'origin': numpy.zeros(3,'d'), + 'homogenization': 0, 'microstructures': 0, - 'homogenization': 0 } newInfo = { 'grid': numpy.zeros(3,'i'), 'size': numpy.zeros(3,'d'), 'microstructures': 0, } + extra_header = [] - new_header = [] - for header in headers: + for header in theTable.info: headitems = map(str.lower,header.split()) - if headitems[0] == 'resolution': headitems[0] = 'grid' - if headitems[0] == 'dimension': headitems[0] = 'size' + if len(headitems) == 0: continue + 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]])): @@ -117,45 +112,63 @@ for file in files: else: info[headitems[0]] = mappings[headitems[0]](headitems[1]) else: - new_header.append(header) + 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\n'%info['microstructures']) - + 'microstructures: %i\n'%info['microstructures']) + if numpy.any(info['grid'] < 1): file['croak'].write('invalid grid a b c.\n') - sys.exit() + continue if numpy.any(info['size'] <= 0.0): file['croak'].write('invalid size x y z.\n') - sys.exit() - - 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['size'] = numpy.array([{True: o*float(n.translate(None,'xX')) , False: float(n.translate(None,'xX'))}[n[-1].lower() == 'x'] for o,n in zip(info['size'],options.size)],'d') - newInfo['grid'] = numpy.where(newInfo['grid'] <= 0 , info['grid'],newInfo['grid']) - newInfo['size'] = numpy.where(newInfo['size'] <= 0.0, info['size'],newInfo['size']) + continue #--- read data ------------------------------------------------------------------------------------ - microstructure = numpy.zeros(info['grid'],'i') + microstructure = numpy.zeros(info['grid'].prod(),'i') i = 0 - for line in content: - items = line.split() + 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) + else: items = map(int,items) + else: items = map(int,items) - for item in items: - microstructure[i%info['grid'][0], - (i/info['grid'][0])%info['grid'][1], - i/info['grid'][0] /info['grid'][1]] = item - i += 1 - newInfo['microstructures'] = microstructure.max() - formatwidth = 1+int(math.floor(math.log10(microstructure.max()))) + s = len(items) + microstructure[i:i+s] = items + i += s + +#--- do work ------------------------------------------------------------------------------------ + + newInfo['grid'] = numpy.array([{True:round(o*float(n.translate(None,'xX'))), False: round(float(n.translate(None,'xX')))}[n[-1].lower() == 'x'] for o,n in zip(info['grid'],options.grid)],'i') + newInfo['size'] = numpy.array([{True: o*float(n.translate(None,'xX')) , False: float(n.translate(None,'xX')) }[n[-1].lower() == 'x'] for o,n in zip(info['size'],options.size)],'d') + newInfo['grid'] = numpy.where(newInfo['grid'] <= 0 , info['grid'],newInfo['grid']) + newInfo['size'] = numpy.where(newInfo['size'] <= 0.0, info['size'],newInfo['size']) + + multiplicity = [] + for j in xrange(3): + multiplicity.append([]) + last = 0 + for i in xrange(info['grid'][j]): + this = int((i+1)*float(newInfo['grid'][j])/info['grid'][j]) + multiplicity[j].append(this-last) + last = this + microstructure = microstructure.reshape(info['grid'],order='F') + microstructure = numpy.repeat( + numpy.repeat( + numpy.repeat(microstructure,multiplicity[0], axis=0), + multiplicity[1], axis=1), + multiplicity[2], axis=2) + + newInfo['microstructures'] = microstructure.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'])): @@ -165,33 +178,33 @@ for file in files: if numpy.any(newInfo['grid'] < 1): file['croak'].write('invalid new grid a b c.\n') - sys.exit() + continue if numpy.any(newInfo['size'] <= 0.0): file['croak'].write('invalid new size x y z.\n') - sys.exit() + continue -#--- assemble header ------------------------------------------------------------------------------ - new_header.append('$Id$\n') - new_header.append("grid\ta %i\tb %i\tc %i\n"%(newInfo['grid'][0],newInfo['grid'][1],newInfo['grid'][2])) - new_header.append("size\tx %f\ty %f\tz %f\n"%(newInfo['size'][0],newInfo['size'][1],newInfo['size'][2])) - new_header.append("origin\tx %f\ty %f\tz %f\n"%(info['origin'][0],info['origin'][1],info['origin'][2])) - new_header.append("microstructures\t%i\n"%newInfo['microstructures']) - new_header.append("homogenization\t%i\n"%info['homogenization']) - file['output'].write('%i\theader\n'%(len(new_header))+''.join(new_header)) +#--- 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"%(info['origin'][0],info['origin'][1],info['origin'][2],), + "homogenization\t%i"%info['homogenization'], + "microstructures\t%i"%(newInfo['microstructures']), + ]) + theTable.head_write() + theTable.output_flush() -#--- scale microstructure ------------------------------------------------------------------------- - for c in xrange(newInfo['grid'][2]): - z = int(info['grid'][2]*(c+0.5)/newInfo['grid'][2])%info['grid'][2] - for b in xrange(newInfo['grid'][1]): - y = int(info['grid'][1]*(b+0.5)/newInfo['grid'][1])%info['grid'][1] - for a in xrange(newInfo['grid'][0]): - x = int(info['grid'][0]*(a+0.5)/newInfo['grid'][0])%info['grid'][0] - file['output'].write(str(microstructure[x,y,z]).rjust(formatwidth) + {True:' ',False:'\n'} - [options.twoD]) - file['output'].write({True:'\n',False:''}[options.twoD]) - +# --- write microstructure information ------------------------------------------------------------ + formatwidth = int(math.floor(math.log10(microstructure.max())+1)) + theTable.data = microstructure.reshape((info['grid'][0],info['grid'][1]*info['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']) - +