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DAMASK_EICMD
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using extendable option, numpy as np, etc.

This commit is contained in:
Martin Diehl 2014-11-07 11:07:03 +00:00
parent 20ed6de76a
commit 047042ad9f
3 changed files with 49 additions and 104 deletions
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78
processing/pre/geom_canvas.py
View File

@ -1,35 +1,19 @@
#!/usr/bin/env python #!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*- # -*- coding: UTF-8 no BOM -*-
import os,sys,string,re,math,numpy import os,re,sys,math,string
import numpy as np
from optparse import OptionParser
import damask import damask
from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
scriptID = '$Id$' scriptID = string.replace('$Id$','\n','\\n')
scriptName = scriptID.split()[1] scriptName = scriptID.split()[1][:-3]
#-------------------------------------------------------------------------------------------------- # --------------------------------------------------------------------
class extendedOption(Option):
#--------------------------------------------------------------------------------------------------
# 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
ACTIONS = Option.ACTIONS + ("extend",)
STORE_ACTIONS = Option.STORE_ACTIONS + ("extend",)
TYPED_ACTIONS = Option.TYPED_ACTIONS + ("extend",)
ALWAYS_TYPED_ACTIONS = Option.ALWAYS_TYPED_ACTIONS + ("extend",)
def take_action(self, action, dest, opt, value, values, parser):
if action == "extend":
lvalue = value.split(",")
values.ensure_value(dest, []).extend(lvalue)
else:
Option.take_action(self, action, dest, opt, value, values, parser)
#--------------------------------------------------------------------------------------------------
# MAIN # MAIN
#-------------------------------------------------------------------------------------------------- # --------------------------------------------------------------------
synonyms = { synonyms = {
'grid': ['resolution'], 'grid': ['resolution'],
'size': ['dimension'], 'size': ['dimension'],
@ -47,17 +31,17 @@ mappings = {
'microstructures': lambda x: int(x), 'microstructures': lambda x: int(x),
} }
parser = OptionParser(option_class=extendedOption, usage='%prog options [file[s]]', description = """ parser = OptionParser(option_class=damask.extendableOption, 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(scriptID,'\n','\\n')
)
parser.add_option('-g', '--grid', dest='grid', nargs = 3, metavar='int int int ', \ """, version = scriptID)
help='a,b,c grid of hexahedral box [unchanged]')
parser.add_option('-o', '--offset', dest='offset', type='int', nargs = 3, metavar='int int int', \ parser.add_option('-g', '--grid', dest='grid', nargs = 3, metavar=' '.join(['string']*3),
help='a,b,c offset from old to new origin of grid %default') help='a,b,c grid of hexahedral box [unchanged]')
parser.add_option('-f', '--fill', dest='fill', type='int', metavar = 'int', \ parser.add_option('-o', '--offset', dest='offset', type='int', nargs = 3, metavar=' '.join(['int']*3),
help='(background) canvas grain index. "0" selects maximum microstructure index + 1 [%default]') help='a,b,c offset from old to new origin of grid %default')
parser.add_option('-f', '--fill', dest='fill', type='int', metavar = 'int',
help='(background) canvas grain index. "0" selects maximum microstructure index + 1 [%default]')
parser.set_defaults(grid = ['0','0','0']) parser.set_defaults(grid = ['0','0','0'])
parser.set_defaults(offset = [0,0,0]) parser.set_defaults(offset = [0,0,0])
@ -92,15 +76,15 @@ for file in files:
#--- interpret header ---------------------------------------------------------------------------- #--- interpret header ----------------------------------------------------------------------------
info = { info = {
'grid': numpy.zeros(3,'i'), 'grid': np.zeros(3,'i'),
'size': numpy.zeros(3,'d'), 'size': np.zeros(3,'d'),
'origin': numpy.zeros(3,'d'), 'origin': np.zeros(3,'d'),
'homogenization': 0, 'homogenization': 0,
'microstructures': 0, 'microstructures': 0,
} }
newInfo = { newInfo = {
'grid': numpy.zeros(3,'i'), 'grid': np.zeros(3,'i'),
'origin': numpy.zeros(3,'d'), 'origin': np.zeros(3,'d'),
'microstructures': 0, 'microstructures': 0,
} }
extra_header = [] extra_header = []
@ -126,15 +110,15 @@ for file in files:
'homogenization: %i\n'%info['homogenization'] + \ 'homogenization: %i\n'%info['homogenization'] + \
'microstructures: %i\n'%info['microstructures']) 'microstructures: %i\n'%info['microstructures'])
if numpy.any(info['grid'] < 1): if np.any(info['grid'] < 1):
file['croak'].write('invalid grid a b c.\n') file['croak'].write('invalid grid a b c.\n')
continue continue
if numpy.any(info['size'] <= 0.0): if np.any(info['size'] <= 0.0):
file['croak'].write('invalid size x y z.\n') file['croak'].write('invalid size x y z.\n')
continue continue
#--- read data ------------------------------------------------------------------------------------ #--- read data ------------------------------------------------------------------------------------
microstructure = numpy.zeros(info['grid'].prod(),'i') # initialize as flat array microstructure = np.zeros(info['grid'].prod(),'i') # initialize as flat array
i = 0 i = 0
theTable.data_rewind() theTable.data_rewind()
while theTable.data_read(): while theTable.data_read():
@ -150,12 +134,12 @@ for file in files:
i += s i += s
#--- do work ------------------------------------------------------------------------------------ #--- do work ------------------------------------------------------------------------------------
newInfo['grid'] = numpy.array([{True: int(o*float(n.translate(None,'xX'))), newInfo['grid'] = np.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') False: int(n.translate(None,'xX'))}[n[-1].lower() == 'x'] for o,n in zip(info['grid'],options.grid)],'i')
newInfo['grid'] = numpy.where(newInfo['grid'] <= 0 , info['grid'],newInfo['grid']) newInfo['grid'] = np.where(newInfo['grid'] <= 0 , info['grid'],newInfo['grid'])
microstructure = microstructure.reshape(info['grid'],order='F') microstructure = microstructure.reshape(info['grid'],order='F')
microstructure_cropped = numpy.zeros(newInfo['grid'],'i') microstructure_cropped = np.zeros(newInfo['grid'],'i')
microstructure_cropped.fill({True:options.fill,False:microstructure.max()+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]+newInfo['grid'][0])) & \ xindex = list(set(xrange(options.offset[0],options.offset[0]+newInfo['grid'][0])) & \
set(xrange(info['grid'][0]))) set(xrange(info['grid'][0])))
@ -189,10 +173,10 @@ for file in files:
if (newInfo['microstructures'] != info['microstructures']): if (newInfo['microstructures'] != info['microstructures']):
file['croak'].write('--> microstructures: %i\n'%newInfo['microstructures']) file['croak'].write('--> microstructures: %i\n'%newInfo['microstructures'])
if numpy.any(newInfo['grid'] < 1): if np.any(newInfo['grid'] < 1):
file['croak'].write('invalid new grid a b c.\n') file['croak'].write('invalid new grid a b c.\n')
continue continue
if numpy.any(newInfo['size'] <= 0.0): if np.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')
continue continue

30
processing/pre/geom_check.py
View File

@ -3,30 +3,11 @@
import os,sys,string,re,vtk import os,sys,string,re,vtk
import numpy as np import numpy as np
from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP from optparse import OptionParser
import damask import damask
scriptID = string.replace('$Id$','\n','\\n') scriptID = string.replace('$Id$','\n','\\n')
scriptName = os.path.splitext(scriptID.split()[1])[0] scriptName = scriptID.split()[1][:-3]
#--------------------------------------------------------------------------------------------------
class extendedOption(Option):
#--------------------------------------------------------------------------------------------------
# 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
ACTIONS = Option.ACTIONS + ("extend",)
STORE_ACTIONS = Option.STORE_ACTIONS + ("extend",)
TYPED_ACTIONS = Option.TYPED_ACTIONS + ("extend",)
ALWAYS_TYPED_ACTIONS = Option.ALWAYS_TYPED_ACTIONS + ("extend",)
def take_action(self, action, dest, opt, value, values, parser):
if action == "extend":
lvalue = value.split(",")
values.ensure_value(dest, []).extend(lvalue)
else:
Option.take_action(self, action, dest, opt, value, values, parser)
#-------------------------------------------------------------------------------------------------- #--------------------------------------------------------------------------------------------------
# MAIN # MAIN
@ -48,11 +29,10 @@ mappings = {
'microstructures': lambda x: int(x), 'microstructures': lambda x: int(x),
} }
parser = OptionParser(option_class=extendedOption, usage='%prog [geomfile[s]]', description = """ parser = OptionParser(option_class=damask.extendableOption, usage='%prog [file[s]]', description = """
Produce VTK rectilinear mesh of structure data from geom description Produce VTK rectilinear mesh of structure data from geom description
""" + string.replace(scriptID,'\n','\\n') """, version = scriptID)
)
parser.add_option('-n','--nodata', dest='data', action='store_false', parser.add_option('-n','--nodata', dest='data', action='store_false',
help='omit microstructure data, just generate mesh') help='omit microstructure data, just generate mesh')
@ -171,7 +151,7 @@ for file in files:
writer.SetDataModeToBinary() writer.SetDataModeToBinary()
writer.SetCompressorTypeToZLib() writer.SetCompressorTypeToZLib()
writer.SetFileName(os.path.join(dir,'mesh_'+os.path.splitext(file)[0] writer.SetFileName(os.path.join(dir,'mesh_'+os.path.splitext(file)[0]
+'.'+writer.GetDefaultFileExtension())) +'.'+writer.GetDefaultFileExtension()))
if vtk.VTK_MAJOR_VERSION <= 5: if vtk.VTK_MAJOR_VERSION <= 5:
writer.SetInput(grid) writer.SetInput(grid)
else: else:

43
processing/pre/seeds_check.py
View File

@ -1,31 +1,13 @@
#!/usr/bin/env python #!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*- # -*- coding: UTF-8 no BOM -*-
import os,sys,string,re,numpy,vtk import os,sys,string,re,vtk
import numpy as np
import damask import damask
from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP from optparse import OptionParser
scriptID = '$Id$'
scriptName = scriptID.split()[1]
#--------------------------------------------------------------------------------------------------
class extendedOption(Option):
#--------------------------------------------------------------------------------------------------
# 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
ACTIONS = Option.ACTIONS + ("extend",)
STORE_ACTIONS = Option.STORE_ACTIONS + ("extend",)
TYPED_ACTIONS = Option.TYPED_ACTIONS + ("extend",)
ALWAYS_TYPED_ACTIONS = Option.ALWAYS_TYPED_ACTIONS + ("extend",)
def take_action(self, action, dest, opt, value, values, parser):
if action == "extend":
lvalue = value.split(",")
values.ensure_value(dest, []).extend(lvalue)
else:
Option.take_action(self, action, dest, opt, value, values, parser)
scriptID = string.replace('$Id$','\n','\\n')
scriptName = scriptID.split()[1][:-3]
#-------------------------------------------------------------------------------------------------- #--------------------------------------------------------------------------------------------------
# MAIN # MAIN
@ -47,11 +29,10 @@ mappings = {
} }
parser = OptionParser(option_class=extendedOption, usage='%prog [seedsfile[s]]', description = """ parser = OptionParser(option_class=damask.extendableOption, usage='%prog [seedsfile[s]]', description = """
Produce VTK point mesh from seeds file Produce VTK point mesh from seeds file
""" + string.replace(scriptID,'\n','\\n') """, version = scriptID)
)
parser.add_option('-g', '--grid', dest='grid', type='int', nargs = 3, metavar='int int int', \ parser.add_option('-g', '--grid', dest='grid', type='int', nargs = 3, metavar='int int int', \
help='a,b,c grid of hexahedral box [from seeds file]') help='a,b,c grid of hexahedral box [from seeds file]')
@ -90,9 +71,9 @@ for file in files:
#--- interpret header ---------------------------------------------------------------------------- #--- interpret header ----------------------------------------------------------------------------
info = { info = {
'grid': numpy.zeros(3,'i'), 'grid': np.zeros(3,'i'),
'size': numpy.zeros(3,'d'), 'size': np.zeros(3,'d'),
'origin': numpy.zeros(3,'d'), 'origin': np.zeros(3,'d'),
} }
for header in theTable.info: for header in theTable.info:
@ -112,8 +93,8 @@ for file in files:
'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']))))
if 0 not in options.grid: # user-specified grid if 0 not in options.grid: # user-specified grid
info['grid'] = numpy.array(options.grid) info['grid'] = np.array(options.grid)
if numpy.any(info['grid'] < 1): if np.any(info['grid'] < 1):
file['croak'].write('invalid grid a b c.\n') file['croak'].write('invalid grid a b c.\n')
# continue # continue