switched to damask.ASCIItable parsing, now aware of synonyms in geometry header, and speed-up by some orders of magnitude due to scipy.ndimage.filters use...
This commit is contained in:
Philip Eisenlohr
parent
2ab3e829a5
commit
463ecfd296
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@ -1,7 +1,8 @@
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#!/usr/bin/env python
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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 os,sys,string,re,math,numpy, damask
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from scipy import ndimage
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from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
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scriptID = '$Id$'
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@ -29,6 +30,11 @@ 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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@ -53,12 +59,9 @@ parser.add_option('-v', '--vicinity', dest='vicinity', type='int', \
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parser.add_option('-m', '--microstructureoffset', dest='offset', type='int', \
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help='offset (positive or negative) for tagged microstructure. '+
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'"0" selects maximum microstructure index [%default]')
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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')
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parser.set_defaults(vicinity = 1)
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parser.set_defaults(offset = 0)
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parser.set_defaults(twoD = False)
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(options, filenames) = parser.parse_args()
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@ -84,36 +87,27 @@ for file in files:
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if file['name'] != 'STDIN': file['croak'].write('\033[1m'+scriptName+'\033[0m: '+file['name']+'\n')
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else: file['croak'].write('\033[1m'+scriptName+'\033[0m\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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'microstructures': 0,
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'homogenization': 0
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}
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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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}
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newInfo = {
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'microstructures': 0,
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}
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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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new_header.append(scriptID+'\n')
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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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@ -122,7 +116,7 @@ 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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@ -132,69 +126,62 @@ for file in files:
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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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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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for item in map(int,line.split()):
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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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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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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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microstructure = microstructure.reshape(info['grid'],order='F')
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if options.offset == 0:
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options.offset = microstructure.max()
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formatwidth = 1+int(math.floor(math.log10(abs(microstructure.max()+options.offset))))
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#--- search ---------------------------------------------------------------------------------------
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for x in xrange(info['grid'][0]):
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for y in xrange(info['grid'][1]):
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for z in xrange(info['grid'][2]):
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me = microstructure[x,y,z]
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breaker = False
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for dx in xrange(-options.vicinity,options.vicinity+1):
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for dy in xrange(-options.vicinity,options.vicinity+1):
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for dz in xrange(-options.vicinity,options.vicinity+1):
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they = microstructure[(x+dx)%info['grid'][0],(y+dy)%info['grid'][1],(z+dz)%info['grid'][2]]
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if they != me and they != me+options.offset: # located alien microstructure in vicinity
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microstructure[x,y,z] += options.offset # tag myself as close to aliens!
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breaker = True
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break
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if breaker: break
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if breaker: break
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microstructure = numpy.where(ndimage.filters.maximum_filter(microstructure,size=1+2*options.vicinity,mode='wrap') ==
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ndimage.filters.minimum_filter(microstructure,size=1+2*options.vicinity,mode='wrap'),
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microstructure, microstructure + options.offset)
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newInfo['microstructures'] = microstructure.max()
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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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# --- assemble header -----------------------------------------------------------------------------
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new_header.append("grid\ta %i\tb %i\tc %i\n"%(info['grid'][0],info['grid'][1],info['grid'][2]))
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new_header.append("size\tx %f\ty %f\tz %f\n"%(info['size'][0],info['size'][1],info['size'][0]))
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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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scriptID,
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"grid\ta %i\tb %i\tc %i"%(info['grid'][0],info['grid'][1],info['grid'][2],),
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"size\tx %f\ty %f\tz %f"%(info['size'][0],info['size'][1],info['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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# --- write microstructure information ------------------------------------------------------------
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for z in xrange(info['grid'][2]):
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for y in xrange(info['grid'][1]):
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file['output'].write({True:' ',False:'\n'}[options.twoD].
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join(map(lambda x: str(x).rjust(formatwidth), microstructure[:,y,z])) + '\n')
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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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file['output'].write('\n')
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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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