now using ASCIItable object and numpy array.repeat --> about 50x faster for large geoms (i.e. several mio voxels).
This commit is contained in:
Philip Eisenlohr
parent
39758f5c53
commit
89cea68bc5
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@ -2,6 +2,7 @@
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# -*- coding: UTF-8 no BOM -*-
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import os,sys,string,re,math,numpy
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import damask
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from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
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#--------------------------------------------------------------------------------------------------
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@ -26,6 +27,10 @@ class extendedOption(Option):
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#--------------------------------------------------------------------------------------------------
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# MAIN
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#--------------------------------------------------------------------------------------------------
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synonyms = {
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'grid': ['resolution'],
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'size': ['dimension'],
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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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@ -41,6 +46,7 @@ mappings = {
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parser = OptionParser(option_class=extendedOption, usage='%prog options [file[s]]', description = """
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Scales a geometry description independently in x, y, and z direction in terms of grid and/or size.
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Either absolute values or relative factors (like "0.25x") can be used.
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""" + string.replace('$Id$','\n','\\n')
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)
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@ -48,12 +54,9 @@ parser.add_option('-g', '--grid', dest='grid', type='string', nargs = 3, \
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help='a,b,c grid of hexahedral box [unchanged]')
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parser.add_option('-s', '--size', dest='size', type='string', nargs = 3, \
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help='x,y,z size of hexahedral box [unchanged]')
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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 [%default]')
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parser.set_defaults(grid = ['0','0','0'])
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parser.set_defaults(size = ['0.0','0.0','0.0'])
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parser.set_defaults(twoD = False)
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(options, filenames) = parser.parse_args()
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@ -78,37 +81,29 @@ else:
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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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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 = [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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theTable = damask.ASCIItable(file['input'],file['output'],labels=False)
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theTable.head_read()
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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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#--- interpret header ----------------------------------------------------------------------------
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info = {
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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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'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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'homogenization': 0,
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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.zeros(3,'i'),
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'size': numpy.zeros(3,'d'),
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'microstructures': 0,
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}
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extra_header = []
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new_header = []
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for header in headers:
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for header in theTable.info:
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headitems = map(str.lower,header.split())
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if headitems[0] == 'resolution': headitems[0] = 'grid'
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if headitems[0] == 'dimension': headitems[0] = 'size'
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if len(headitems) == 0: continue
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for synonym,alternatives in synonyms.iteritems():
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if headitems[0] in alternatives: headitems[0] = synonym
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if headitems[0] in mappings.keys():
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if headitems[0] in identifiers.keys():
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for i in xrange(len(identifiers[headitems[0]])):
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@ -117,45 +112,63 @@ 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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else:
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new_header.append(header)
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extra_header.append(header)
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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\n'%info['microstructures'])
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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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continue
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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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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')
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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')
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newInfo['grid'] = numpy.where(newInfo['grid'] <= 0 , info['grid'],newInfo['grid'])
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newInfo['size'] = numpy.where(newInfo['size'] <= 0.0, info['size'],newInfo['size'])
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continue
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#--- read data ------------------------------------------------------------------------------------
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microstructure = numpy.zeros(info['grid'],'i')
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microstructure = numpy.zeros(info['grid'].prod(),'i')
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i = 0
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for line in content:
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items = line.split()
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theTable.data_rewind()
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while theTable.data_read():
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items = theTable.data
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if len(items) > 2:
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if items[1].lower() == 'of': items = [int(items[2])]*int(items[0])
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elif items[1].lower() == 'to': items = xrange(int(items[0]),1+int(items[2]))
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else: items = map(int,items)
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else: items = map(int,items)
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else: items = map(int,items)
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else: items = map(int,items)
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for item in items:
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microstructure[i%info['grid'][0],
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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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newInfo['microstructures'] = microstructure.max()
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formatwidth = 1+int(math.floor(math.log10(microstructure.max())))
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s = len(items)
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microstructure[i:i+s] = items
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i += s
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#--- do work ------------------------------------------------------------------------------------
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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')
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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')
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newInfo['grid'] = numpy.where(newInfo['grid'] <= 0 , info['grid'],newInfo['grid'])
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newInfo['size'] = numpy.where(newInfo['size'] <= 0.0, info['size'],newInfo['size'])
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multiplicity = []
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for j in xrange(3):
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multiplicity.append([])
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last = 0
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for i in xrange(info['grid'][j]):
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this = int((i+1)*float(newInfo['grid'][j])/info['grid'][j])
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multiplicity[j].append(this-last)
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last = this
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microstructure = microstructure.reshape(info['grid'],order='F')
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microstructure = numpy.repeat(
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numpy.repeat(
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numpy.repeat(microstructure,multiplicity[0], axis=0),
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multiplicity[1], axis=1),
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multiplicity[2], axis=2)
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newInfo['microstructures'] = microstructure.max()
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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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@ -165,33 +178,33 @@ for file in files:
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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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continue
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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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continue
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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"%(newInfo['grid'][0],newInfo['grid'][1],newInfo['grid'][2]))
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new_header.append("size\tx %f\ty %f\tz %f\n"%(newInfo['size'][0],newInfo['size'][1],newInfo['size'][2]))
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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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file['output'].write('%i\theader\n'%(len(new_header))+''.join(new_header))
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#--- write header ---------------------------------------------------------------------------------
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theTable.labels_clear()
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theTable.info_clear()
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theTable.info_append(extra_header+[
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"$Id$",
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"grid\ta %i\tb %i\tc %i"%(newInfo['grid'][0],newInfo['grid'][1],newInfo['grid'][2],),
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"size\tx %f\ty %f\tz %f"%(newInfo['size'][0],newInfo['size'][1],newInfo['size'][2],),
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"origin\tx %f\ty %f\tz %f"%(info['origin'][0],info['origin'][1],info['origin'][2],),
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"homogenization\t%i"%info['homogenization'],
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"microstructures\t%i"%(newInfo['microstructures']),
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])
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theTable.head_write()
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theTable.output_flush()
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#--- scale microstructure -------------------------------------------------------------------------
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for c in xrange(newInfo['grid'][2]):
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z = int(info['grid'][2]*(c+0.5)/newInfo['grid'][2])%info['grid'][2]
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for b in xrange(newInfo['grid'][1]):
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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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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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# --- write microstructure information ------------------------------------------------------------
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formatwidth = int(math.floor(math.log10(microstructure.max())+1))
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theTable.data = microstructure.reshape((info['grid'][0],info['grid'][1]*info['grid'][2]),order='F').transpose()
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theTable.data_writeArray('%%%ii'%(formatwidth))
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#--- output finalization --------------------------------------------------------------------------
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if file['name'] != 'STDIN':
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file['input'].close()
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file['output'].close()
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os.rename(file['name']+'_tmp',file['name'])
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