now based on damask.ASCIItable object
continue with next if one file is broken (used to stop!) packing of already packed works now overall speed improvement standard unpacked output is 2D: use -1/--onedimensional for linear list
This commit is contained in:
Philip Eisenlohr
parent
fcc2736431
commit
77aa1c27b0
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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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@ -67,30 +68,23 @@ 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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'microstructures': 0,
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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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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
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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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@ -100,31 +94,52 @@ 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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new_header.append(header)
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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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'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'%info['microstructures'])
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'microstructures: %i\n\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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continue
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file['output'].write('%i\theader\n'%(len(new_header))+''.join(new_header))
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#--- pack input -----------------------------------------------------------------------------------
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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"%(info['origin'][0],info['origin'][1],info['origin'][2],),
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"microstructures\t%i"%(info['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 packed microstructure information ------------------------------------------------------------
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type = ''
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former = -1
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start = -1
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reps = 0
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for line in content:
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for current in map(int,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 current in items:
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if current == former+1 and start+reps == former+1:
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type = 'to'
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reps += 1
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@ -132,24 +147,30 @@ for file in files:
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type = 'of'
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reps += 1
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else:
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output = {'': '',
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'.': str(former)+'\n',
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'to': '%i to %i\n'%(former-reps+1,former),
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'of': '%i of %i\n'%(reps,former),
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}[type]
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file['output'].write(output)
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theTable.data = {
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'' : [],
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'.' : [str(former)],
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'to': ['%i to %i'%(former-reps+1,former)],
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'of': ['%i of %i'%(reps,former)],
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}[type]
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theTable.data_write()
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# file['output'].write(output)
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type = '.'
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start = current
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reps = 1
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former = current
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output = {'.': str(former),
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'to': '%i to %i'%(former-reps+1,former),
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'of': '%i of %i'%(reps,former),
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}[type]
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file['output'].write(output+'\n')
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theTable.data = {
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'.' : [str(former)],
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'to': ['%i to %i'%(former-reps+1,former)],
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'of': ['%i of %i'%(reps,former)],
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}[type]
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theTable.data_write()
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theTable.output_flush()
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# file['output'].write(output+'\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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@ -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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@ -44,10 +45,10 @@ Unpack geometry files containing ranges "a to b" and/or "n of x" multiples (excl
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""" + string.replace('$Id$','\n','\\n')
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)
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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.add_option('-1', '--onedimensional', dest='oneD', action='store_true', \
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help='output geom file with one-dimensional data arrangement [%default]')
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parser.set_defaults(twoD = False)
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parser.set_defaults(oneD = False)
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(options, filenames) = parser.parse_args()
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@ -68,34 +69,27 @@ 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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'homogenization': 0,
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'microstructures': 0,
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'homogenization': 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
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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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@ -105,45 +99,62 @@ 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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new_header.append(header)
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format = {True: info['grid'][0],
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False: 1}[options.twoD]
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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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'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'%info['microstructures'])
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'microstructures: %i\n\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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continue
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file['output'].write('%i\theader\n'%(len(new_header))+''.join(new_header))
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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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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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if info['microstructures'] > 0:
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digits = 1+int(math.log10(int(info['microstructures'])))
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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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#--- 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"%(info['origin'][0],info['origin'][1],info['origin'][2],),
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"microstructures\t%i"%(info['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(microstructure.max())+1))
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if options.oneD:
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theTable.data = microstructure
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else:
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digits = 1+int(math.log10(int(info['grid'][0]*info['grid'][1]*info['grid'][2])))
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#--- unpack input ---------------------------------------------------------------------------------
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wordsWritten = 0
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for line in content:
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words = line.split()
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if len(words) > 2: # any packing keywords?
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if words[1].lower() == 'to': words = map(str,range(int(words[0]),int(words[2])+1))
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elif words[1].lower() == 'of': words = [words[2]]*int(words[0])
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for word in words:
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wordsWritten += 1
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file['output'].write(word.rjust(digits)+{True:'\n',False:' '}[wordsWritten%format == 0]) # newline every format words
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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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