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DAMASK_EICMD
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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 2013-06-30 19:11:16 +00:00
parent 39758f5c53
commit 89cea68bc5
1 changed files with 80 additions and 67 deletions
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131
processing/pre/geom_rescale.py
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@ -2,6 +2,7 @@
# -*- coding: UTF-8 no BOM -*- # -*- coding: UTF-8 no BOM -*-
import os,sys,string,re,math,numpy import os,sys,string,re,math,numpy
import damask
from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
#-------------------------------------------------------------------------------------------------- #--------------------------------------------------------------------------------------------------
@ -26,6 +27,10 @@ class extendedOption(Option):
#-------------------------------------------------------------------------------------------------- #--------------------------------------------------------------------------------------------------
# MAIN # MAIN
#-------------------------------------------------------------------------------------------------- #--------------------------------------------------------------------------------------------------
synonyms = {
'grid': ['resolution'],
'size': ['dimension'],
}
identifiers = { identifiers = {
'grid': ['a','b','c'], 'grid': ['a','b','c'],
'size': ['x','y','z'], 'size': ['x','y','z'],
@ -41,6 +46,7 @@ mappings = {
parser = OptionParser(option_class=extendedOption, usage='%prog options [file[s]]', description = """ parser = OptionParser(option_class=extendedOption, usage='%prog options [file[s]]', description = """
Scales a geometry description independently in x, y, and z direction in terms of grid and/or size. Scales a geometry description independently in x, y, and z direction in terms of grid and/or size.
Either absolute values or relative factors (like "0.25x") can be used.
""" + string.replace('$Id$','\n','\\n') """ + string.replace('$Id$','\n','\\n')
) )
@ -48,12 +54,9 @@ parser.add_option('-g', '--grid', dest='grid', type='string', nargs = 3, \
help='a,b,c grid of hexahedral box [unchanged]') help='a,b,c grid of hexahedral box [unchanged]')
parser.add_option('-s', '--size', dest='size', type='string', nargs = 3, \ parser.add_option('-s', '--size', dest='size', type='string', nargs = 3, \
help='x,y,z size of hexahedral box [unchanged]') help='x,y,z size of hexahedral box [unchanged]')
parser.add_option('-2', '--twodimensional', dest='twoD', action='store_true', \
help='output geom file with two-dimensional data arrangement [%default]')
parser.set_defaults(grid = ['0','0','0']) parser.set_defaults(grid = ['0','0','0'])
parser.set_defaults(size = ['0.0','0.0','0.0']) parser.set_defaults(size = ['0.0','0.0','0.0'])
parser.set_defaults(twoD = False)
(options, filenames) = parser.parse_args() (options, filenames) = parser.parse_args()
@ -78,37 +81,29 @@ else:
for file in files: for file in files:
if file['name'] != 'STDIN': file['croak'].write(file['name']+'\n') if file['name'] != 'STDIN': file['croak'].write(file['name']+'\n')
firstline = file['input'].readline() theTable = damask.ASCIItable(file['input'],file['output'],labels=False)
m = re.search('(\d+)\s*head', firstline.lower()) theTable.head_read()
if m:
headerlines = int(m.group(1))
headers = [file['input'].readline() for i in range(headerlines)]
else:
headerlines = 1
headers = firstline
content = file['input'].readlines() #--- interpret header ----------------------------------------------------------------------------
file['input'].close()
#--- interprete header ----------------------------------------------------------------------------
info = { info = {
'grid': numpy.zeros(3,'i'), 'grid': numpy.zeros(3,'i'),
'size': numpy.zeros(3,'d'), 'size': numpy.zeros(3,'d'),
'origin': numpy.zeros(3,'d'), 'origin': numpy.zeros(3,'d'),
'homogenization': 0,
'microstructures': 0, 'microstructures': 0,
'homogenization': 0
} }
newInfo = { newInfo = {
'grid': numpy.zeros(3,'i'), 'grid': numpy.zeros(3,'i'),
'size': numpy.zeros(3,'d'), 'size': numpy.zeros(3,'d'),
'microstructures': 0, 'microstructures': 0,
} }
extra_header = []
new_header = [] for header in theTable.info:
for header in headers:
headitems = map(str.lower,header.split()) headitems = map(str.lower,header.split())
if headitems[0] == 'resolution': headitems[0] = 'grid' if len(headitems) == 0: continue
if headitems[0] == 'dimension': headitems[0] = 'size' for synonym,alternatives in synonyms.iteritems():
if headitems[0] in alternatives: headitems[0] = synonym
if headitems[0] in mappings.keys(): if headitems[0] in mappings.keys():
if headitems[0] in identifiers.keys(): if headitems[0] in identifiers.keys():
for i in xrange(len(identifiers[headitems[0]])): for i in xrange(len(identifiers[headitems[0]])):
@ -117,45 +112,63 @@ for file in files:
else: else:
info[headitems[0]] = mappings[headitems[0]](headitems[1]) info[headitems[0]] = mappings[headitems[0]](headitems[1])
else: else:
new_header.append(header) extra_header.append(header)
file['croak'].write('grid a b c: %s\n'%(' x '.join(map(str,info['grid']))) + \ file['croak'].write('grid a b c: %s\n'%(' x '.join(map(str,info['grid']))) + \
'size x y z: %s\n'%(' x '.join(map(str,info['size']))) + \ 'size x y z: %s\n'%(' x '.join(map(str,info['size']))) + \
'origin x y z: %s\n'%(' : '.join(map(str,info['origin']))) + \ 'origin x y z: %s\n'%(' : '.join(map(str,info['origin']))) + \
'homogenization: %i\n'%info['homogenization'] + \ 'homogenization: %i\n'%info['homogenization'] + \
'microstructures: %i\n\n'%info['microstructures']) 'microstructures: %i\n'%info['microstructures'])
if numpy.any(info['grid'] < 1): if numpy.any(info['grid'] < 1):
file['croak'].write('invalid grid a b c.\n') file['croak'].write('invalid grid a b c.\n')
sys.exit() continue
if numpy.any(info['size'] <= 0.0): if numpy.any(info['size'] <= 0.0):
file['croak'].write('invalid size x y z.\n') file['croak'].write('invalid size x y z.\n')
sys.exit() continue
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')
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')
newInfo['grid'] = numpy.where(newInfo['grid'] <= 0 , info['grid'],newInfo['grid'])
newInfo['size'] = numpy.where(newInfo['size'] <= 0.0, info['size'],newInfo['size'])
#--- read data ------------------------------------------------------------------------------------ #--- read data ------------------------------------------------------------------------------------
microstructure = numpy.zeros(info['grid'],'i') microstructure = numpy.zeros(info['grid'].prod(),'i')
i = 0 i = 0
for line in content: theTable.data_rewind()
items = line.split() while theTable.data_read():
items = theTable.data
if len(items) > 2: if len(items) > 2:
if items[1].lower() == 'of': items = [int(items[2])]*int(items[0]) if items[1].lower() == 'of': items = [int(items[2])]*int(items[0])
elif items[1].lower() == 'to': items = xrange(int(items[0]),1+int(items[2])) elif items[1].lower() == 'to': items = xrange(int(items[0]),1+int(items[2]))
else: items = map(int,items) else: items = map(int,items)
else: items = map(int,items) else: items = map(int,items)
for item in items: s = len(items)
microstructure[i%info['grid'][0], microstructure[i:i+s] = items
(i/info['grid'][0])%info['grid'][1], i += s
i/info['grid'][0] /info['grid'][1]] = item
i += 1
newInfo['microstructures'] = microstructure.max()
formatwidth = 1+int(math.floor(math.log10(microstructure.max())))
#--- do work ------------------------------------------------------------------------------------
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')
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')
newInfo['grid'] = numpy.where(newInfo['grid'] <= 0 , info['grid'],newInfo['grid'])
newInfo['size'] = numpy.where(newInfo['size'] <= 0.0, info['size'],newInfo['size'])
multiplicity = []
for j in xrange(3):
multiplicity.append([])
last = 0
for i in xrange(info['grid'][j]):
this = int((i+1)*float(newInfo['grid'][j])/info['grid'][j])
multiplicity[j].append(this-last)
last = this
microstructure = microstructure.reshape(info['grid'],order='F')
microstructure = numpy.repeat(
numpy.repeat(
numpy.repeat(microstructure,multiplicity[0], axis=0),
multiplicity[1], axis=1),
multiplicity[2], axis=2)
newInfo['microstructures'] = microstructure.max()
#--- report ---------------------------------------------------------------------------------------
if (any(newInfo['grid'] != info['grid'])): if (any(newInfo['grid'] != info['grid'])):
file['croak'].write('--> grid a b c: %s\n'%(' x '.join(map(str,newInfo['grid'])))) file['croak'].write('--> grid a b c: %s\n'%(' x '.join(map(str,newInfo['grid']))))
if (any(newInfo['size'] != info['size'])): if (any(newInfo['size'] != info['size'])):
@ -165,33 +178,33 @@ for file in files:
if numpy.any(newInfo['grid'] < 1): if numpy.any(newInfo['grid'] < 1):
file['croak'].write('invalid new grid a b c.\n') file['croak'].write('invalid new grid a b c.\n')
sys.exit() continue
if numpy.any(newInfo['size'] <= 0.0): if numpy.any(newInfo['size'] <= 0.0):
file['croak'].write('invalid new size x y z.\n') file['croak'].write('invalid new size x y z.\n')
sys.exit() continue
#--- assemble header ------------------------------------------------------------------------------ #--- write header ---------------------------------------------------------------------------------
new_header.append('$Id$\n') theTable.labels_clear()
new_header.append("grid\ta %i\tb %i\tc %i\n"%(newInfo['grid'][0],newInfo['grid'][1],newInfo['grid'][2])) theTable.info_clear()
new_header.append("size\tx %f\ty %f\tz %f\n"%(newInfo['size'][0],newInfo['size'][1],newInfo['size'][2])) theTable.info_append(extra_header+[
new_header.append("origin\tx %f\ty %f\tz %f\n"%(info['origin'][0],info['origin'][1],info['origin'][2])) "$Id$",
new_header.append("microstructures\t%i\n"%newInfo['microstructures']) "grid\ta %i\tb %i\tc %i"%(newInfo['grid'][0],newInfo['grid'][1],newInfo['grid'][2],),
new_header.append("homogenization\t%i\n"%info['homogenization']) "size\tx %f\ty %f\tz %f"%(newInfo['size'][0],newInfo['size'][1],newInfo['size'][2],),
file['output'].write('%i\theader\n'%(len(new_header))+''.join(new_header)) "origin\tx %f\ty %f\tz %f"%(info['origin'][0],info['origin'][1],info['origin'][2],),
"homogenization\t%i"%info['homogenization'],
"microstructures\t%i"%(newInfo['microstructures']),
])
theTable.head_write()
theTable.output_flush()
#--- scale microstructure ------------------------------------------------------------------------- # --- write microstructure information ------------------------------------------------------------
for c in xrange(newInfo['grid'][2]): formatwidth = int(math.floor(math.log10(microstructure.max())+1))
z = int(info['grid'][2]*(c+0.5)/newInfo['grid'][2])%info['grid'][2] theTable.data = microstructure.reshape((info['grid'][0],info['grid'][1]*info['grid'][2]),order='F').transpose()
for b in xrange(newInfo['grid'][1]): theTable.data_writeArray('%%%ii'%(formatwidth))
y = int(info['grid'][1]*(b+0.5)/newInfo['grid'][1])%info['grid'][1]
for a in xrange(newInfo['grid'][0]):
x = int(info['grid'][0]*(a+0.5)/newInfo['grid'][0])%info['grid'][0]
file['output'].write(str(microstructure[x,y,z]).rjust(formatwidth) + {True:' ',False:'\n'}
[options.twoD])
file['output'].write({True:'\n',False:''}[options.twoD])
#--- output finalization -------------------------------------------------------------------------- #--- output finalization --------------------------------------------------------------------------
if file['name'] != 'STDIN': if file['name'] != 'STDIN':
file['input'].close()
file['output'].close() file['output'].close()
os.rename(file['name']+'_tmp',file['name']) os.rename(file['name']+'_tmp',file['name'])