now based on damask.ASCIItable object
continue with next if one file is broken (used to stop!) improved index substitution and adopted more numpy functions --> notably faster
This commit is contained in:
Philip Eisenlohr
parent
f204c38d4d
commit
fcc2736431
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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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@ -83,19 +84,10 @@ 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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@ -104,12 +96,14 @@ for file in files:
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'homogenization': 0
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}
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newInfo = {
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'origin': numpy.zeros(3,'d'),
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'origin': numpy.zeros(3,'d'),
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'microstructures': 0,
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}
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new_header = []
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for header in headers:
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extra_header = []
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for header in theTable.info:
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headitems = map(str.lower,header.split())
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if len(headitems) == 0: continue
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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 headitems[0] in mappings.keys():
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@ -120,8 +114,7 @@ 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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@ -131,63 +124,66 @@ 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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#--- process input --------------------------------------------------------------------------------
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N = info['grid'].prod()
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microstructure = numpy.zeros(N,'i')
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continue
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#--- read data ------------------------------------------------------------------------------------
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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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s = len(items)
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microstructure[i:i+s] = items # read microstructure indices
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microstructure[i:i+s] = items
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i += s
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for i in xrange(N):
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if microstructure[i] in sub: microstructure[i] = sub[microstructure[i]] # substitute microstructure indices
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#--- do work ------------------------------------------------------------------------------------
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substituted = numpy.copy(microstructure)
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for k, v in sub.iteritems(): substituted[microstructure==k] = v # substitute microstructure indices
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# for i in xrange(N):
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# if microstructure[i] in sub: microstructure[i] = sub[microstructure[i]] # substitute microstructure indices
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microstructure += options.microstructure # shift microstructure indices
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formatwidth = int(math.floor(math.log10(microstructure.max())+1))
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substituted += options.microstructure # shift microstructure indices
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#--- assemble header and report changes -----------------------------------------------------------
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newInfo['origin'] = info['origin'] + options.origin
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newInfo['microstructures'] = microstructure.max()
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newInfo['microstructures'] = substituted.max()
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#--- report ---------------------------------------------------------------------------------------
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if (any(newInfo['origin'] != info['origin'])):
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file['croak'].write('--> origin x y z: %s\n'%(' : '.join(map(str,newInfo['origin']))))
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file['croak'].write('--> origin x y z: %s\n'%(' : '.join(map(str,newInfo['origin']))))
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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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new_header.append('$Id$\n')
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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'][2],))
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new_header.append("origin\tx %f\ty %f\tz %f\n"%(
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newInfo['origin'][0],newInfo['origin'][1],newInfo['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 new data -------------------------------------------------------------------------------
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i = 0
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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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output = {True:' ',False:'\n'}[options.twoD].join(map(lambda x: ('%%%ii'%formatwidth)%x,
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microstructure[i:i+info['grid'][0]])) + '\n'
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file['output'].write(output)
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i += info['grid'][0]
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#--- output finalization --------------------------------------------------------------------------
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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"%(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"%(newInfo['origin'][0],newInfo['origin'][1],newInfo['origin'][2],),
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"microstructures\t%i"%(newInfo['microstructures']),
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"homogenization\t%i"%info['homogenization'],
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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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formatwidth = int(math.floor(math.log10(substituted.max())+1))
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theTable.data = substituted.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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