now based on damask.ASCIItable object
continue with next if one file is broken (used to stop!) switched to numpy functions for geom reshaping and writing --> 10x faster
This commit is contained in:
Philip Eisenlohr
parent
7d6035dcfa
commit
f204c38d4d
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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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@ -50,12 +51,9 @@ parser.add_option('-o', '--offset', dest='offset', type='int', nargs = 3, \
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help='a,b,c offset from old to new origin of grid %default')
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parser.add_option('-f', '--fill', dest='fill', type='int', \
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help='(background) canvas grain index. "0" selects maximum microstructure index + 1 [%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 [%default]')
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parser.set_defaults(grid = ['0','0','0'])
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parser.set_defaults(offset = [0,0,0])
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parser.set_defaults(twoD = False)
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parser.set_defaults(fill = 0)
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(options, filenames) = parser.parse_args()
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@ -77,38 +75,31 @@ else:
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'croak':sys.stdout,
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})
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#--- loop over input files ------------------------------------------------------------------------
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#--- loop over input files ------------------------------------------------------------------------
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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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'microstructures': 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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'origin': 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 len(headitems) == 0: continue # skip blank lines
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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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@ -118,6 +109,8 @@ for file in files:
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mappings[headitems[0]](headitems[headitems.index(identifiers[headitems[0]][i])+1])
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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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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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@ -127,31 +120,32 @@ 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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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['grid'] = numpy.where(newInfo['grid'] <= 0 , info['grid'],newInfo['grid'])
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#--- read data ------------------------------------------------------------------------------------
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microstructure = numpy.zeros(info['grid'],'i')
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#--- read data ------------------------------------------------------------------------------------
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microstructure = numpy.zeros(info['grid'].prod(),'i') # initialize as flat array
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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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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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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: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['grid'] = numpy.where(newInfo['grid'] <= 0 , info['grid'],newInfo['grid'])
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microstructure = microstructure.reshape(info['grid'],order='F')
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microstructure_cropped = numpy.zeros(newInfo['grid'],'i')
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microstructure_cropped.fill({True:options.fill,False:microstructure.max()+1}[options.fill>0])
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xindex = list(set(xrange(options.offset[0],options.offset[0]+newInfo['grid'][0])) & \
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@ -169,11 +163,11 @@ for file in files:
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= microstructure[min(xindex):(max(xindex)+1),\
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min(yindex):(max(yindex)+1),\
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min(zindex):(max(zindex)+1)]
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formatwidth = int(math.floor(math.log10(microstructure.max())+1))
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newInfo['microstructures'] = microstructure_cropped.max()
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newInfo['size'] = info['size']/info['grid']*newInfo['grid']
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newInfo['origin'] = info['origin']+info['size']/info['grid']*options.offset
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newInfo['microstructures'] = microstructure_cropped.max()
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#--- report ---------------------------------------------------------------------------------------
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@ -188,30 +182,32 @@ 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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# --- 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"%(
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newInfo['grid'][0],newInfo['grid'][1],newInfo['grid'][2]))
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new_header.append("size\tx %f\ty %f\tz %f\n"%(
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newInfo['size'][0],newInfo['size'][1],newInfo['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("homogenization\t%i\n"%info['homogenization'])
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new_header.append("microstructures\t%i\n"%newInfo['microstructures'])
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file['output'].write('%i\theader\n'%(len(new_header))+''.join(new_header))
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continue
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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"%(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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for z in xrange(newInfo['grid'][2]):
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for y in xrange(newInfo['grid'][1]):
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file['output'].write({True:' ',False:'\n'}[options.twoD].join(map(lambda x: \
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('%%%ii'%formatwidth)%x, microstructure_cropped[:,y,z])) + '\n')
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formatwidth = int(math.floor(math.log10(microstructure_cropped.max())+1))
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theTable.data = microstructure_cropped.reshape((newInfo['grid'][0],newInfo['grid'][1]*newInfo['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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