using extendable option, numpy as np, etc.
This commit is contained in:
Martin Diehl
parent
047042ad9f
commit
2d2eb4e001
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@ -1,34 +1,16 @@
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#!/usr/bin/env python
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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 os,re,sys,math,string
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import numpy as np
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from optparse import OptionParser
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import damask
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from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
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scriptID = '$Id: geom_addPrimitive.py 3412 2014-08-22 16:58:53Z MPIE\m.diehl $'
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scriptName = scriptID.split()[1]
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scriptID = string.replace('$Id: geom_pack.py 3679 2014-11-05 22:01:11Z p.eisenlohr $','\n','\\n')
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scriptName = scriptID.split()[1][:-3]
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oversampling = 2.
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#--------------------------------------------------------------------------------------------------
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class extendedOption(Option):
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#--------------------------------------------------------------------------------------------------
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# used for definition of new option parser action 'extend', which enables to take multiple option arguments
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# taken from online tutorial http://docs.python.org/library/optparse.html
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ACTIONS = Option.ACTIONS + ("extend",)
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STORE_ACTIONS = Option.STORE_ACTIONS + ("extend",)
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TYPED_ACTIONS = Option.TYPED_ACTIONS + ("extend",)
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ALWAYS_TYPED_ACTIONS = Option.ALWAYS_TYPED_ACTIONS + ("extend",)
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def take_action(self, action, dest, opt, value, values, parser):
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if action == "extend":
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lvalue = value.split(",")
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values.ensure_value(dest, []).extend(lvalue)
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else:
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Option.take_action(self, action, dest, opt, value, values, parser)
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#--------------------------------------------------------------------------------------------------
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# MAIN
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#--------------------------------------------------------------------------------------------------
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@ -49,11 +31,11 @@ mappings = {
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'microstructures': lambda x: int(x),
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}
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parser = OptionParser(option_class=extendedOption, usage='%prog options [file[s]]', description = """
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parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
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Positions a geometric object within the (three-dimensional) canvas of a spectral geometry description.
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Depending on the sign of the dimension parameters, these objects can be boxes, cylinders, or ellipsoids.
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""" + string.replace(scriptID,'\n','\\n')
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)
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""", version = scriptID)
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parser.add_option('-o', '--origin',
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'-c', '--center', dest='center', type='int', nargs = 3, metavar=' '.join(['int']*3),
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@ -80,7 +62,7 @@ parser.set_defaults(center = [0,0,0],
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if options.angleaxis != []:
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options.angleaxis = map(float,options.angleaxis)
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rotation = damask.Quaternion().fromAngleAxis(numpy.radians(options.angleaxis[0]) if options.degrees else options.angleaxis[0],
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rotation = damask.Quaternion().fromAngleAxis(np.radians(options.angleaxis[0]) if options.degrees else options.angleaxis[0],
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options.angleaxis[1:4]).conjugated()
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elif options.quaternion != []:
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options.rotation = map(float,options.rotation)
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@ -88,7 +70,7 @@ elif options.quaternion != []:
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else:
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rotation = damask.Quaternion().conjugated()
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options.center = numpy.array(options.center)
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options.center = np.array(options.center)
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invRotation = rotation.conjugated() # rotation of gridpos into primitive coordinate system
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#--- setup file handles --------------------------------------------------------------------------
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@ -118,15 +100,15 @@ for file in files:
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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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'grid': np.zeros(3,'i'),
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'size': np.zeros(3,'d'),
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'origin': np.zeros(3,'d'),
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'homogenization': 0,
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'microstructures': 0,
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}
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newInfo = {
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'grid': numpy.zeros(3,'i'),
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'origin': numpy.zeros(3,'d'),
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'grid': np.zeros(3,'i'),
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'origin': np.zeros(3,'d'),
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'microstructures': 0,
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}
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extra_header = []
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@ -152,15 +134,15 @@ for file in files:
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'homogenization: %i\n'%info['homogenization'] + \
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'microstructures: %i\n'%info['microstructures'])
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if numpy.any(info['grid'] < 1):
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if np.any(info['grid'] < 1):
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file['croak'].write('invalid grid a b c.\n')
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continue
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if numpy.any(info['size'] <= 0.0):
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if np.any(info['size'] <= 0.0):
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file['croak'].write('invalid size x y z.\n')
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continue
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#--- read data ------------------------------------------------------------------------------------
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microstructure = numpy.zeros(info['grid'].prod(),'i') # initialize as flat array
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microstructure = np.zeros(info['grid'].prod(),'i') # initialize as flat array
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i = 0
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while table.data_read():
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@ -183,17 +165,17 @@ for file in files:
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microstructure = microstructure.reshape(info['grid'],order='F')
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if options.dimension != None:
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mask = (numpy.array(options.dimension) < 0).astype(float) # zero where positive dimension, otherwise one
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dim = abs(numpy.array(options.dimension)) # dimensions of primitive body
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pos = numpy.zeros(3,dtype='float')
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# hiresPrimitive = numpy.zeros((2*dim[0],2*dim[1],2*dim[2],3)) # primitive discretized at twice the grid resolution
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for i,pos[0] in enumerate(numpy.arange(-dim[0]/oversampling,(dim[0]+1)/oversampling,1./oversampling)):
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for j,pos[1] in enumerate(numpy.arange(-dim[1]/oversampling,(dim[1]+1)/oversampling,1./oversampling)):
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for k,pos[2] in enumerate(numpy.arange(-dim[2]/oversampling,(dim[2]+1)/oversampling,1./oversampling)):
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gridpos = numpy.floor(rotation*pos) # rotate and lock into spacial grid
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mask = (np.array(options.dimension) < 0).astype(float) # zero where positive dimension, otherwise one
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dim = abs(np.array(options.dimension)) # dimensions of primitive body
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pos = np.zeros(3,dtype='float')
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# hiresPrimitive = np.zeros((2*dim[0],2*dim[1],2*dim[2],3)) # primitive discretized at twice the grid resolution
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for i,pos[0] in enumerate(np.arange(-dim[0]/oversampling,(dim[0]+1)/oversampling,1./oversampling)):
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for j,pos[1] in enumerate(np.arange(-dim[1]/oversampling,(dim[1]+1)/oversampling,1./oversampling)):
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for k,pos[2] in enumerate(np.arange(-dim[2]/oversampling,(dim[2]+1)/oversampling,1./oversampling)):
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gridpos = np.floor(rotation*pos) # rotate and lock into spacial grid
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primPos = invRotation*gridpos # rotate back to primitive coordinate system
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if numpy.dot(mask*primPos/dim,mask*primPos/dim) <= 0.25 and \
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numpy.all(abs((1.-mask)*primPos/dim) <= 0.5): # inside ellipsoid and inside box
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if np.dot(mask*primPos/dim,mask*primPos/dim) <= 0.25 and \
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np.all(abs((1.-mask)*primPos/dim) <= 0.5): # inside ellipsoid and inside box
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microstructure[(gridpos[0]+options.center[0])%info['grid'][0],
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(gridpos[1]+options.center[1])%info['grid'][1],
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(gridpos[2]+options.center[2])%info['grid'][2]] = options.fill # assign microstructure index
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@ -1,31 +1,13 @@
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#!/usr/bin/env python
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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 os,sys,string,re,math
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import numpy as np
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from optparse import OptionParser
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import damask
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from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
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scriptID = '$Id$'
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scriptName = scriptID.split()[1]
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#--------------------------------------------------------------------------------------------------
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class extendedOption(Option):
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#--------------------------------------------------------------------------------------------------
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# used for definition of new option parser action 'extend', which enables to take multiple option arguments
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# taken from online tutorial http://docs.python.org/library/optparse.html
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ACTIONS = Option.ACTIONS + ("extend",)
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STORE_ACTIONS = Option.STORE_ACTIONS + ("extend",)
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TYPED_ACTIONS = Option.TYPED_ACTIONS + ("extend",)
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ALWAYS_TYPED_ACTIONS = Option.ALWAYS_TYPED_ACTIONS + ("extend",)
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def take_action(self, action, dest, opt, value, values, parser):
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if action == "extend":
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lvalue = value.split(",")
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values.ensure_value(dest, []).extend(lvalue)
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else:
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Option.take_action(self, action, dest, opt, value, values, parser)
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scriptID = string.replace('$Id$','\n','\\n')
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scriptName = scriptID.split()[1][:-3]
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#--------------------------------------------------------------------------------------------------
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# MAIN
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@ -47,11 +29,11 @@ mappings = {
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'microstructures': lambda x: int(x),
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}
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parser = OptionParser(option_class=extendedOption, usage='%prog options [file[s]]', description = """
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parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
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Scales a geometry description independently in x, y, and z direction in terms of grid and/or size.
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Either absolute values or relative factors (like "0.25x") can be used.
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""" + string.replace(scriptID,'\n','\\n')
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)
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""", version = scriptID)
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parser.add_option('-g', '--grid', dest='grid', nargs = 3, metavar = 'string string string', \
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help='a,b,c grid of hexahedral box [unchanged]')
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@ -93,15 +75,15 @@ for file in files:
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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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'grid': np.zeros(3,'i'),
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'size': np.zeros(3,'d'),
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'origin': np.zeros(3,'d'),
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'homogenization': 0,
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'microstructures': 0,
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}
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newInfo = {
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'grid': numpy.zeros(3,'i'),
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'size': numpy.zeros(3,'d'),
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'grid': np.zeros(3,'i'),
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'size': np.zeros(3,'d'),
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'microstructures': 0,
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}
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extra_header = []
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@ -127,15 +109,15 @@ for file in files:
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'homogenization: %i\n'%info['homogenization'] + \
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'microstructures: %i\n'%info['microstructures'])
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if numpy.any(info['grid'] < 1):
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if np.any(info['grid'] < 1):
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file['croak'].write('invalid grid a b c.\n')
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continue
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if numpy.any(info['size'] <= 0.0):
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if np.any(info['size'] <= 0.0):
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file['croak'].write('invalid size x y z.\n')
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continue
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#--- read data ------------------------------------------------------------------------------------
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microstructure = numpy.zeros(info['grid'].prod(),'i')
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microstructure = np.zeros(info['grid'].prod(),'i')
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i = 0
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table.data_rewind()
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while table.data_read():
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@ -152,10 +134,10 @@ for file in files:
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#--- do work ------------------------------------------------------------------------------------
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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')
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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')
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newInfo['grid'] = numpy.where(newInfo['grid'] <= 0 , info['grid'],newInfo['grid'])
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newInfo['size'] = numpy.where(newInfo['size'] <= 0.0, info['size'],newInfo['size'])
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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')
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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')
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newInfo['grid'] = np.where(newInfo['grid'] <= 0 , info['grid'],newInfo['grid'])
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newInfo['size'] = np.where(newInfo['size'] <= 0.0, info['size'],newInfo['size'])
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multiplicity = []
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for j in xrange(3):
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@ -167,19 +149,19 @@ for file in files:
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last = this
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microstructure = microstructure.reshape(info['grid'],order='F')
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microstructure = numpy.repeat(
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numpy.repeat(
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numpy.repeat(microstructure,multiplicity[0], axis=0),
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microstructure = np.repeat(
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np.repeat(
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np.repeat(microstructure,multiplicity[0], axis=0),
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multiplicity[1], axis=1),
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multiplicity[2], axis=2)
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# --- renumber to sequence 1...Ngrains if requested ------------------------------------------------
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# http://stackoverflow.com/questions/10741346/numpy-frequency-counts-for-unique-values-in-an-array
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# http://stackoverflow.com/questions/10741346/np-frequency-counts-for-unique-values-in-an-array
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if options.renumber:
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newID=0
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for microstructureID,count in enumerate(numpy.bincount(microstructure.reshape(newInfo['grid'].prod()))):
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for microstructureID,count in enumerate(np.bincount(microstructure.reshape(newInfo['grid'].prod()))):
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if count != 0:
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newID+=1
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microstructure=numpy.where(microstructure==microstructureID,newID,microstructure).reshape(microstructure.shape)
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microstructure=np.where(microstructure==microstructureID,newID,microstructure).reshape(microstructure.shape)
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newInfo['microstructures'] = microstructure.max()
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@ -191,10 +173,10 @@ for file in files:
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if (newInfo['microstructures'] != info['microstructures']):
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file['croak'].write('--> microstructures: %i\n'%newInfo['microstructures'])
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if numpy.any(newInfo['grid'] < 1):
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if np.any(newInfo['grid'] < 1):
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file['croak'].write('invalid new grid a b c.\n')
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continue
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if numpy.any(newInfo['size'] <= 0.0):
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if np.any(newInfo['size'] <= 0.0):
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file['croak'].write('invalid new size x y z.\n')
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continue
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