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DAMASK_EICMD
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still improving preprocessing scripts

This commit is contained in:
Martin Diehl 2013-05-15 17:23:21 +00:00
parent 190a59b707
commit 17b81fda7c
4 changed files with 82 additions and 72 deletions
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122
processing/pre/geom_canvas.py
View File

@ -4,10 +4,9 @@
import os,sys,string,re,math,numpy import os,sys,string,re,math,numpy
from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
#--------------------------------------------------------------------------------------------------
# -----------------------------
class extendedOption(Option): class extendedOption(Option):
# ----------------------------- #--------------------------------------------------------------------------------------------------
# used for definition of new option parser action 'extend', which enables to take multiple option arguments # used for definition of new option parser action 'extend', which enables to take multiple option arguments
# taken from online tutorial http://docs.python.org/library/optparse.html # taken from online tutorial http://docs.python.org/library/optparse.html
@ -24,8 +23,9 @@ class extendedOption(Option):
Option.take_action(self, action, dest, opt, value, values, parser) Option.take_action(self, action, dest, opt, value, values, parser)
# ----------------------- MAIN ------------------------------- #--------------------------------------------------------------------------------------------------
# MAIN
#--------------------------------------------------------------------------------------------------
identifiers = { identifiers = {
'grid': ['a','b','c'], 'grid': ['a','b','c'],
'size': ['x','y','z'], 'size': ['x','y','z'],
@ -38,7 +38,6 @@ mappings = {
'homogenization': lambda x: int(x), 'homogenization': lambda x: int(x),
} }
parser = OptionParser(option_class=extendedOption, usage='%prog options [file[s]]', description = """ parser = OptionParser(option_class=extendedOption, usage='%prog options [file[s]]', description = """
Changes the (three-dimensional) canvas of a spectral geometry description. Changes the (three-dimensional) canvas of a spectral geometry description.
""" + string.replace('$Id$','\n','\\n') """ + string.replace('$Id$','\n','\\n')
@ -60,7 +59,7 @@ parser.set_defaults(fill = 0)
(options, filenames) = parser.parse_args() (options, filenames) = parser.parse_args()
# ------------------------------------------ setup file handles --------------------------------------- #--- setup file handles --------------------------------------------------------------------------
files = [] files = []
if filenames == []: if filenames == []:
files.append({'name':'STDIN', files.append({'name':'STDIN',
@ -77,13 +76,10 @@ else:
'croak':sys.stdout, 'croak':sys.stdout,
}) })
# ------------------------------------------ loop over input files --------------------------------------- #--- loop over input files ------------------------------------------------------------------------
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')
# get labels by either read the first row, or - if keyword header is present - the last line of the header
firstline = file['input'].readline() firstline = file['input'].readline()
m = re.search('(\d+)\s*head', firstline.lower()) m = re.search('(\d+)\s*head', firstline.lower())
if m: if m:
@ -96,13 +92,20 @@ for file in files:
content = file['input'].readlines() content = file['input'].readlines()
file['input'].close() file['input'].close()
#--- interprete header ----------------------------------------------------------------------------
info = { info = {
'grid': numpy.array(options.grid), 'grid': numpy.zeros(3,'i'),
'size': numpy.array([0.0,0.0,0.0]), 'size': numpy.zeros(3,'d'),
'origin': numpy.array([0.0,0.0,0.0]), 'origin': numpy.zeros(3,'d'),
'microstructures': 0, 'microstructures': 0,
'homogenization': 0, 'homogenization': 0,
} }
newInfo = {
'grid': numpy.array(options.grid),
'size': numpy.zeros(3,'d'),
'origin': numpy.zeros(3,'d'),
'microstructures': 0,
}
new_header = [] new_header = []
for header in headers: for header in headers:
@ -117,15 +120,20 @@ for file in files:
else: else:
info[headitems[0]] = mappings[headitems[0]](headitems[1]) info[headitems[0]] = mappings[headitems[0]](headitems[1])
if numpy.all(options.grid == 0): file['croak'].write('grid a b c: %s\n'%(' x '.join(map(str,info['grid']))) + \
options.grid = info['grid'] 'size x y z: %s\n'%(' x '.join(map(str,info['size']))) + \
if numpy.all(info['grid'] == 0): 'origin x y z: %s\n'%(' : '.join(map(str,info['origin']))) + \
file['croak'].write('no grid info found.\n') 'homogenization: %i\n'%info['homogenization'] + \
continue 'microstructures: %i\n'%info['microstructures'])
if numpy.all(info['size'] == 0.0):
file['croak'].write('no size info found.\n')
continue
if numpy.any(info['grid'] < 1):
file['croak'].write('invalid grid a b c.\n')
sys.exit()
if numpy.any(info['size'] <= 0.0):
file['croak'].write('invalid size x y z.\n')
sys.exit()
#--- read data ------------------------------------------------------------------------------------
microstructure = numpy.zeros(info['grid'],'i') microstructure = numpy.zeros(info['grid'],'i')
i = 0 i = 0
for line in content: for line in content:
@ -135,25 +143,8 @@ for file in files:
i/info['grid'][0] /info['grid'][1]] = item i/info['grid'][0] /info['grid'][1]] = item
i += 1 i += 1
file['croak'].write('-- input --\n' + \
'grid a b c: %s\n'%(' x '.join(map(str,info['grid']))) + \
'size x y z: %s\n'%(' x '.join(map(str,info['size']))) + \
'origin x y z: %s\n'%(' : '.join(map(str,info['origin']))) + \
'homogenization: %i\n'%info['homogenization'] + \
'microstructures: %i\n'%info['microstructures'])
info['microstructures'] = microstructure.max()
newSize = info['size']/info['grid']*options.grid
newOrigin = info['origin']+info['size']/info['grid']*options.offset
new_header.append("grid\ta %i\tb %i\tc %i\n"%(options.grid[0],options.grid[1],options.grid[2]))
new_header.append("size\tx %f\ty %f\tz %f\n"%(newSize[0],newSize[1],newSize[2]))
new_header.append("origin\tx %f\ty %f\tz %f\n"%(newOrigin[0],newOrigin[1],newOrigin[2]))
new_header.append("homogenization\t%i\n"%info['homogenization'])
new_header.append("microstructures\t%i\n"%info['microstructures'])
microstructure_cropped = numpy.zeros(options.grid,'i') microstructure_cropped = numpy.zeros(options.grid,'i')
microstructure_cropped.fill({True:options.fill,False:info['microstructures']+1}[options.fill>0]) microstructure_cropped.fill({True:options.fill,False:microstructure.max()+1}[options.fill>0])
xindex = list(set(xrange(options.offset[0],options.offset[0]+options.grid[0])) & \ xindex = list(set(xrange(options.offset[0],options.offset[0]+options.grid[0])) & \
set(xrange(info['grid'][0]))) set(xrange(info['grid'][0])))
yindex = list(set(xrange(options.offset[1],options.offset[1]+options.grid[1])) & \ yindex = list(set(xrange(options.offset[1],options.offset[1]+options.grid[1])) & \
@ -171,28 +162,49 @@ for file in files:
min(zindex):(max(zindex)+1)] min(zindex):(max(zindex)+1)]
formatwidth = int(math.floor(math.log10(microstructure.max())+1)) formatwidth = int(math.floor(math.log10(microstructure.max())+1))
file['croak'].write('-- output --\n' +\ if numpy.all(options.grid == 0):
'grid a b c: %s\n'%(' x '.join(map(str,options.grid))) + \ newInfo['grid'] = info['grid']
'size x y z: %s\n'%(' x '.join(map(str,newSize))) + \ newInfo['microstructures'] = microstructure_cropped.max()
'origin x y z: %s\n'%(' x '.join(map(str,newOrigin))) + \ newInfo['size'] = info['size']/info['grid']*options.grid
'microstructures: %i\n'%microstructure.max()) newInfo['origin'] = info['origin']+info['size']/info['grid']*options.offset
# ------------------------------------------ assemble header ---------------------------------------
output = '%i\theader\n'%(len(new_header)) #--- report ---------------------------------------------------------------------------------------
output += ''.join(new_header) if (any(newInfo['grid'] != info['grid'])):
file['croak'].write('--> grid a b c: %s\n'%(' x '.join(map(str,newInfo['grid']))))
if (any(newInfo['size'] != info['size'])):
file['croak'].write('--> size x y z: %s\n'%(' x '.join(map(str,newInfo['size']))))
if (any(newInfo['origin'] != info['origin'])):
file['croak'].write('--> origin x y z: %s\n'%(' : '.join(map(str,newInfo['size']))))
if (newInfo['microstructures'] != info['microstructures']):
file['croak'].write('--> microstructures: %i\n'%newInfo['microstructures'])
# ------------------------------------- regenerate texture information ---------------------------- if numpy.any(newInfo['grid'] < 1):
file['croak'].write('invalid new grid a b c.\n')
sys.exit()
if numpy.any(newInfo['size'] <= 0.0):
file['croak'].write('invalid new size x y z.\n')
sys.exit()
# --- assemble header -----------------------------------------------------------------------------
new_header.append('$Id$\n')
new_header.append("grid\ta %i\tb %i\tc %i\n"%(
newInfo['grid'][0],newInfo['grid'][1],newInfo['grid'][2]))
new_header.append("size\tx %f\ty %f\tz %f\n"%(
newInfo['size'][0],newInfo['size'][1],newInfo['size'][2]))
new_header.append("origin\tx %f\ty %f\tz %f\n"%(
newInfo['origin'][0],newInfo['origin'][1],newInfo['origin'][2]))
new_header.append("homogenization\t%i\n"%info['homogenization'])
new_header.append("microstructures\t%i\n"%newInfo['microstructures'])
file['output'].write('%i\theader\n'%(len(new_header))+''.join(new_header))
# --- write microstructure information ------------------------------------------------------------
for z in xrange(options.grid[2]): for z in xrange(options.grid[2]):
for y in xrange(options.grid[1]): for y in xrange(options.grid[1]):
output += {True:' ',False:'\n'}[options.twoD].join(map(lambda x: \ file['output'].write({True:' ',False:'\n'}[options.twoD].join(map(lambda x: \
('%%%ii'%formatwidth)%x, microstructure_cropped[:,y,z])) + '\n' ('%%%ii'%formatwidth)%x, microstructure_cropped[:,y,z])) + '\n')
# ------------------------------------------ output result ---------------------------------------
file['output'].write(output)
#--- output finalization --------------------------------------------------------------------------
if file['name'] != 'STDIN': if file['name'] != 'STDIN':
file['output'].close() file['output'].close()
os.rename(file['name']+'_tmp',file['name']) os.rename(file['name']+'_tmp',file['name'])

1
processing/pre/geom_fromVoronoiTessellation.py
View File

@ -212,7 +212,6 @@ for file in files:
join(map(lambda x: str(x).rjust(formatwidth),\ join(map(lambda x: str(x).rjust(formatwidth),\
indices[n*info['grid'][0]:(n+1)*info['grid'][0]]))+'\n') indices[n*info['grid'][0]:(n+1)*info['grid'][0]]))+'\n')
#--- output finalization -------------------------------------------------------------------------- #--- output finalization --------------------------------------------------------------------------
if file['name'] != 'STDIN': if file['name'] != 'STDIN':
file['output'].close() file['output'].close()

19
processing/pre/geom_rescale.py
View File

@ -126,15 +126,15 @@ for file in files:
'microstructures: %i\n\n'%info['microstructures']) 'microstructures: %i\n\n'%info['microstructures'])
if numpy.any(info['grid'] < 1): if numpy.any(info['grid'] < 1):
file['croak'].write('no valid grid info found.\n') file['croak'].write('invalid grid a b c.\n')
sys.exit() sys.exit()
if numpy.any(info['size'] <= 0.0): if numpy.any(info['size'] <= 0.0):
file['croak'].write('no valid size info found.\n') file['croak'].write('invalid size x y z.\n')
sys.exit() sys.exit()
if numpy.all(info['grid'] == 0): if numpy.all(info['grid'] == 0):
newInfo['grid'] = info['grid'] newInfo['grid'] = info['grid']
if numpy.all(info['size'] == 0.0):: if numpy.all(info['size'] == 0.0):
newInfo['size'] = info['size'] newInfo['size'] = info['size']
#--- read data ------------------------------------------------------------------------------------ #--- read data ------------------------------------------------------------------------------------
@ -157,10 +157,10 @@ for file in files:
file['croak'].write('--> microstructures: %i\n'%newInfo['microstructures']) file['croak'].write('--> microstructures: %i\n'%newInfo['microstructures'])
if numpy.any(newInfo['grid'] < 1): if numpy.any(newInfo['grid'] < 1):
file['croak'].write('no valid new grid info found.\n') file['croak'].write('invalid new grid a b c.\n')
sys.exit() sys.exit()
if numpy.any(newInfo['size'] <= 0.0): if numpy.any(newInfo['size'] <= 0.0):
file['croak'].write('no valid new size info found.\n') file['croak'].write('invalid new size x y z.\n')
sys.exit() sys.exit()
#--- assemble header ------------------------------------------------------------------------------ #--- assemble header ------------------------------------------------------------------------------
@ -170,8 +170,7 @@ for file in files:
new_header.append("origin\tx %f\ty %f\tz %f\n"%(info['origin'][0],info['origin'][1],info['origin'][2])) new_header.append("origin\tx %f\ty %f\tz %f\n"%(info['origin'][0],info['origin'][1],info['origin'][2]))
new_header.append("microstructures\t%i\n"%newInfo['microstructures']) new_header.append("microstructures\t%i\n"%newInfo['microstructures'])
new_header.append("homogenization\t%i\n"%info['homogenization']) new_header.append("homogenization\t%i\n"%info['homogenization'])
output = '%i\theader\n'%(len(new_header)) file['output'].write('%i\theader\n'%(len(new_header))+''.join(new_header))
output += ''.join(new_header)
#--- scale microstructure ------------------------------------------------------------------------- #--- scale microstructure -------------------------------------------------------------------------
for c in xrange(newInfo['grid'][2]): for c in xrange(newInfo['grid'][2]):
@ -180,9 +179,9 @@ for file in files:
y = int(info['grid'][1]*(b+0.5)/newInfo['grid'][1])%info['grid'][1] y = int(info['grid'][1]*(b+0.5)/newInfo['grid'][1])%info['grid'][1]
for a in xrange(newInfo['grid'][0]): for a in xrange(newInfo['grid'][0]):
x = int(info['grid'][0]*(a+0.5)/newInfo['grid'][0])%info['grid'][0] x = int(info['grid'][0]*(a+0.5)/newInfo['grid'][0])%info['grid'][0]
output += str(microstructure[x,y,z]).rjust(formatwidth) + {True:' ',False:'\n'}[options.twoD] file['output'].write(str(microstructure[x,y,z]).rjust(formatwidth) + {True:' ',False:'\n'}
output += {True:'\n',False:''}[options.twoD] [options.twoD])
file['output'].write(output) file['output'].write({True:'\n',False:''}[options.twoD])
#--- output finalization -------------------------------------------------------------------------- #--- output finalization --------------------------------------------------------------------------
if file['name'] != 'STDIN': if file['name'] != 'STDIN':

6
processing/pre/geom_translate.py
View File

@ -130,14 +130,14 @@ for file in files:
'microstructures: %i\n\n'%info['microstructures']) 'microstructures: %i\n\n'%info['microstructures'])
if numpy.any(info['grid'] < 1): if numpy.any(info['grid'] < 1):
file['croak'].write('no valid grid info found.\n') file['croak'].write('invalid grid a b c.\n')
sys.exit() sys.exit()
if numpy.any(info['size'] <= 0.0): if numpy.any(info['size'] <= 0.0):
file['croak'].write('no valid size info found.\n') file['croak'].write('invalid size x y z.\n')
sys.exit() sys.exit()
#--- process input -------------------------------------------------------------------------------- #--- process input --------------------------------------------------------------------------------
N = info['grid'][0]*info['grid'][1]*info['grid'][2] N = info['grid'].prod()
microstructure = numpy.zeros(N,'i') microstructure = numpy.zeros(N,'i')
i = 0 i = 0