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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 11:13:14 +00:00
parent 047042ad9f
commit 2d2eb4e001
2 changed files with 56 additions and 92 deletions
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74
processing/pre/geom_addPrimitive.py
View File

@ -1,34 +1,16 @@
#!/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: geom_addPrimitive.py 3412 2014-08-22 16:58:53Z MPIE\m.diehl $' scriptID = string.replace('$Id: geom_pack.py 3679 2014-11-05 22:01:11Z p.eisenlohr $','\n','\\n')
scriptName = scriptID.split()[1] scriptName = scriptID.split()[1][:-3]
oversampling = 2. oversampling = 2.
#--------------------------------------------------------------------------------------------------
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
#-------------------------------------------------------------------------------------------------- #--------------------------------------------------------------------------------------------------
@ -49,11 +31,11 @@ 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 = """
Positions a geometric object within the (three-dimensional) canvas of a spectral geometry description. Positions a geometric object within the (three-dimensional) canvas of a spectral geometry description.
Depending on the sign of the dimension parameters, these objects can be boxes, cylinders, or ellipsoids. Depending on the sign of the dimension parameters, these objects can be boxes, cylinders, or ellipsoids.
""" + string.replace(scriptID,'\n','\\n')
) """, version = scriptID)
parser.add_option('-o', '--origin', parser.add_option('-o', '--origin',
'-c', '--center', dest='center', type='int', nargs = 3, metavar=' '.join(['int']*3), '-c', '--center', dest='center', type='int', nargs = 3, metavar=' '.join(['int']*3),
@ -80,7 +62,7 @@ parser.set_defaults(center = [0,0,0],
if options.angleaxis != []: if options.angleaxis != []:
options.angleaxis = map(float,options.angleaxis) options.angleaxis = map(float,options.angleaxis)
rotation = damask.Quaternion().fromAngleAxis(numpy.radians(options.angleaxis[0]) if options.degrees else options.angleaxis[0], rotation = damask.Quaternion().fromAngleAxis(np.radians(options.angleaxis[0]) if options.degrees else options.angleaxis[0],
options.angleaxis[1:4]).conjugated() options.angleaxis[1:4]).conjugated()
elif options.quaternion != []: elif options.quaternion != []:
options.rotation = map(float,options.rotation) options.rotation = map(float,options.rotation)
@ -88,7 +70,7 @@ elif options.quaternion != []:
else: else:
rotation = damask.Quaternion().conjugated() rotation = damask.Quaternion().conjugated()
options.center = numpy.array(options.center) options.center = np.array(options.center)
invRotation = rotation.conjugated() # rotation of gridpos into primitive coordinate system invRotation = rotation.conjugated() # rotation of gridpos into primitive coordinate system
#--- setup file handles -------------------------------------------------------------------------- #--- setup file handles --------------------------------------------------------------------------
@ -118,15 +100,15 @@ 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 = []
@ -152,15 +134,15 @@ 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
while table.data_read(): while table.data_read():
@ -183,17 +165,17 @@ for file in files:
microstructure = microstructure.reshape(info['grid'],order='F') microstructure = microstructure.reshape(info['grid'],order='F')
if options.dimension != None: if options.dimension != None:
mask = (numpy.array(options.dimension) < 0).astype(float) # zero where positive dimension, otherwise one mask = (np.array(options.dimension) < 0).astype(float) # zero where positive dimension, otherwise one
dim = abs(numpy.array(options.dimension)) # dimensions of primitive body dim = abs(np.array(options.dimension)) # dimensions of primitive body
pos = numpy.zeros(3,dtype='float') pos = np.zeros(3,dtype='float')
# hiresPrimitive = numpy.zeros((2*dim[0],2*dim[1],2*dim[2],3)) # primitive discretized at twice the grid resolution # hiresPrimitive = np.zeros((2*dim[0],2*dim[1],2*dim[2],3)) # primitive discretized at twice the grid resolution
for i,pos[0] in enumerate(numpy.arange(-dim[0]/oversampling,(dim[0]+1)/oversampling,1./oversampling)): for i,pos[0] in enumerate(np.arange(-dim[0]/oversampling,(dim[0]+1)/oversampling,1./oversampling)):
for j,pos[1] in enumerate(numpy.arange(-dim[1]/oversampling,(dim[1]+1)/oversampling,1./oversampling)): for j,pos[1] in enumerate(np.arange(-dim[1]/oversampling,(dim[1]+1)/oversampling,1./oversampling)):
for k,pos[2] in enumerate(numpy.arange(-dim[2]/oversampling,(dim[2]+1)/oversampling,1./oversampling)): for k,pos[2] in enumerate(np.arange(-dim[2]/oversampling,(dim[2]+1)/oversampling,1./oversampling)):
gridpos = numpy.floor(rotation*pos) # rotate and lock into spacial grid gridpos = np.floor(rotation*pos) # rotate and lock into spacial grid
primPos = invRotation*gridpos # rotate back to primitive coordinate system primPos = invRotation*gridpos # rotate back to primitive coordinate system
if numpy.dot(mask*primPos/dim,mask*primPos/dim) <= 0.25 and \ if np.dot(mask*primPos/dim,mask*primPos/dim) <= 0.25 and \
numpy.all(abs((1.-mask)*primPos/dim) <= 0.5): # inside ellipsoid and inside box np.all(abs((1.-mask)*primPos/dim) <= 0.5): # inside ellipsoid and inside box
microstructure[(gridpos[0]+options.center[0])%info['grid'][0], microstructure[(gridpos[0]+options.center[0])%info['grid'][0],
(gridpos[1]+options.center[1])%info['grid'][1], (gridpos[1]+options.center[1])%info['grid'][1],
(gridpos[2]+options.center[2])%info['grid'][2]] = options.fill # assign microstructure index (gridpos[2]+options.center[2])%info['grid'][2]] = options.fill # assign microstructure index

74
processing/pre/geom_rescale.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,math,numpy import os,sys,string,re,math
import numpy as np
from optparse import OptionParser
import damask import damask
from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
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 +29,11 @@ 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 = """
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. Either absolute values or relative factors (like "0.25x") can be used.
""" + string.replace(scriptID,'\n','\\n')
) """, version = scriptID)
parser.add_option('-g', '--grid', dest='grid', nargs = 3, metavar = 'string string string', \ parser.add_option('-g', '--grid', dest='grid', nargs = 3, metavar = 'string string string', \
help='a,b,c grid of hexahedral box [unchanged]') help='a,b,c grid of hexahedral box [unchanged]')
@ -93,15 +75,15 @@ 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'),
'size': numpy.zeros(3,'d'), 'size': np.zeros(3,'d'),
'microstructures': 0, 'microstructures': 0,
} }
extra_header = [] extra_header = []
@ -127,15 +109,15 @@ 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') microstructure = np.zeros(info['grid'].prod(),'i')
i = 0 i = 0
table.data_rewind() table.data_rewind()
while table.data_read(): while table.data_read():
@ -152,10 +134,10 @@ for file in files:
#--- do work ------------------------------------------------------------------------------------ #--- 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['grid'] = np.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['size'] = np.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['grid'] = np.where(newInfo['grid'] <= 0 , info['grid'],newInfo['grid'])
newInfo['size'] = numpy.where(newInfo['size'] <= 0.0, info['size'],newInfo['size']) newInfo['size'] = np.where(newInfo['size'] <= 0.0, info['size'],newInfo['size'])
multiplicity = [] multiplicity = []
for j in xrange(3): for j in xrange(3):
@ -167,19 +149,19 @@ for file in files:
last = this last = this
microstructure = microstructure.reshape(info['grid'],order='F') microstructure = microstructure.reshape(info['grid'],order='F')
microstructure = numpy.repeat( microstructure = np.repeat(
numpy.repeat( np.repeat(
numpy.repeat(microstructure,multiplicity[0], axis=0), np.repeat(microstructure,multiplicity[0], axis=0),
multiplicity[1], axis=1), multiplicity[1], axis=1),
multiplicity[2], axis=2) multiplicity[2], axis=2)
# --- renumber to sequence 1...Ngrains if requested ------------------------------------------------ # --- renumber to sequence 1...Ngrains if requested ------------------------------------------------
# http://stackoverflow.com/questions/10741346/numpy-frequency-counts-for-unique-values-in-an-array # http://stackoverflow.com/questions/10741346/np-frequency-counts-for-unique-values-in-an-array
if options.renumber: if options.renumber:
newID=0 newID=0
for microstructureID,count in enumerate(numpy.bincount(microstructure.reshape(newInfo['grid'].prod()))): for microstructureID,count in enumerate(np.bincount(microstructure.reshape(newInfo['grid'].prod()))):
if count != 0: if count != 0:
newID+=1 newID+=1
microstructure=numpy.where(microstructure==microstructureID,newID,microstructure).reshape(microstructure.shape) microstructure=np.where(microstructure==microstructureID,newID,microstructure).reshape(microstructure.shape)
newInfo['microstructures'] = microstructure.max() newInfo['microstructures'] = microstructure.max()
@ -191,10 +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