using extendable option, numpy as np, etc.
This commit is contained in:
parent
20ed6de76a
commit
047042ad9f
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@ -1,35 +1,19 @@
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#!/usr/bin/env python
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#!/usr/bin/env python
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# -*- coding: UTF-8 no BOM -*-
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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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import damask
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from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
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scriptID = '$Id$'
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scriptID = string.replace('$Id$','\n','\\n')
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scriptName = scriptID.split()[1]
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scriptName = scriptID.split()[1][:-3]
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#--------------------------------------------------------------------------------------------------
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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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# MAIN
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#--------------------------------------------------------------------------------------------------
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# --------------------------------------------------------------------
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synonyms = {
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synonyms = {
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'grid': ['resolution'],
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'grid': ['resolution'],
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'size': ['dimension'],
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'size': ['dimension'],
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@ -47,17 +31,17 @@ mappings = {
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'microstructures': lambda x: int(x),
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'microstructures': lambda x: int(x),
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}
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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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Changes the (three-dimensional) canvas of a spectral geometry description.
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Changes the (three-dimensional) canvas of a spectral geometry description.
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""" + string.replace(scriptID,'\n','\\n')
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)
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parser.add_option('-g', '--grid', dest='grid', nargs = 3, metavar='int int int ', \
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""", version = scriptID)
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help='a,b,c grid of hexahedral box [unchanged]')
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parser.add_option('-o', '--offset', dest='offset', type='int', nargs = 3, metavar='int int int', \
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parser.add_option('-g', '--grid', dest='grid', nargs = 3, metavar=' '.join(['string']*3),
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help='a,b,c offset from old to new origin of grid %default')
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help='a,b,c grid of hexahedral box [unchanged]')
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parser.add_option('-f', '--fill', dest='fill', type='int', metavar = 'int', \
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parser.add_option('-o', '--offset', dest='offset', type='int', nargs = 3, metavar=' '.join(['int']*3),
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help='(background) canvas grain index. "0" selects maximum microstructure index + 1 [%default]')
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help='a,b,c offset from old to new origin of grid %default')
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parser.add_option('-f', '--fill', dest='fill', type='int', metavar = 'int',
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help='(background) canvas grain index. "0" selects maximum microstructure index + 1 [%default]')
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parser.set_defaults(grid = ['0','0','0'])
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parser.set_defaults(grid = ['0','0','0'])
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parser.set_defaults(offset = [0,0,0])
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parser.set_defaults(offset = [0,0,0])
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@ -92,15 +76,15 @@ for file in files:
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#--- interpret header ----------------------------------------------------------------------------
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#--- interpret header ----------------------------------------------------------------------------
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info = {
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info = {
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'grid': numpy.zeros(3,'i'),
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'grid': np.zeros(3,'i'),
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'size': numpy.zeros(3,'d'),
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'size': np.zeros(3,'d'),
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'origin': numpy.zeros(3,'d'),
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'origin': np.zeros(3,'d'),
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'homogenization': 0,
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'homogenization': 0,
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'microstructures': 0,
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'microstructures': 0,
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}
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}
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newInfo = {
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newInfo = {
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'grid': numpy.zeros(3,'i'),
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'grid': np.zeros(3,'i'),
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'origin': numpy.zeros(3,'d'),
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'origin': np.zeros(3,'d'),
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'microstructures': 0,
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'microstructures': 0,
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}
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}
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extra_header = []
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extra_header = []
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@ -126,15 +110,15 @@ for file in files:
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'homogenization: %i\n'%info['homogenization'] + \
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'homogenization: %i\n'%info['homogenization'] + \
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'microstructures: %i\n'%info['microstructures'])
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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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file['croak'].write('invalid grid a b c.\n')
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continue
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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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file['croak'].write('invalid size x y z.\n')
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continue
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continue
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#--- read data ------------------------------------------------------------------------------------
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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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i = 0
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theTable.data_rewind()
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theTable.data_rewind()
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while theTable.data_read():
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while theTable.data_read():
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@ -150,12 +134,12 @@ for file in files:
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i += s
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i += s
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#--- do work ------------------------------------------------------------------------------------
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#--- do work ------------------------------------------------------------------------------------
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newInfo['grid'] = numpy.array([{True: int(o*float(n.translate(None,'xX'))),
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newInfo['grid'] = np.array([{True: int(o*float(n.translate(None,'xX'))),
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False: int(n.translate(None,'xX'))}[n[-1].lower() == 'x'] for o,n in zip(info['grid'],options.grid)],'i')
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False: int(n.translate(None,'xX'))}[n[-1].lower() == 'x'] for o,n in zip(info['grid'],options.grid)],'i')
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newInfo['grid'] = numpy.where(newInfo['grid'] <= 0 , info['grid'],newInfo['grid'])
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newInfo['grid'] = np.where(newInfo['grid'] <= 0 , info['grid'],newInfo['grid'])
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microstructure = microstructure.reshape(info['grid'],order='F')
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microstructure = microstructure.reshape(info['grid'],order='F')
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microstructure_cropped = numpy.zeros(newInfo['grid'],'i')
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microstructure_cropped = np.zeros(newInfo['grid'],'i')
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microstructure_cropped.fill({True:options.fill,False:microstructure.max()+1}[options.fill>0])
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microstructure_cropped.fill({True:options.fill,False:microstructure.max()+1}[options.fill>0])
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xindex = list(set(xrange(options.offset[0],options.offset[0]+newInfo['grid'][0])) & \
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xindex = list(set(xrange(options.offset[0],options.offset[0]+newInfo['grid'][0])) & \
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set(xrange(info['grid'][0])))
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set(xrange(info['grid'][0])))
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@ -189,10 +173,10 @@ for file in files:
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if (newInfo['microstructures'] != info['microstructures']):
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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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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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file['croak'].write('invalid new grid a b c.\n')
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continue
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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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file['croak'].write('invalid new size x y z.\n')
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continue
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continue
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@ -3,31 +3,12 @@
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import os,sys,string,re,vtk
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import os,sys,string,re,vtk
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import numpy as np
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import numpy as np
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from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
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from optparse import OptionParser
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import damask
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import damask
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scriptID = string.replace('$Id$','\n','\\n')
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scriptID = string.replace('$Id$','\n','\\n')
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scriptName = os.path.splitext(scriptID.split()[1])[0]
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scriptName = scriptID.split()[1][:-3]
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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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#--------------------------------------------------------------------------------------------------
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# MAIN
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# MAIN
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#--------------------------------------------------------------------------------------------------
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#--------------------------------------------------------------------------------------------------
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@ -48,11 +29,10 @@ mappings = {
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'microstructures': lambda x: int(x),
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'microstructures': lambda x: int(x),
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}
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}
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parser = OptionParser(option_class=extendedOption, usage='%prog [geomfile[s]]', description = """
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parser = OptionParser(option_class=damask.extendableOption, usage='%prog [file[s]]', description = """
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Produce VTK rectilinear mesh of structure data from geom description
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Produce VTK rectilinear mesh of structure data from geom description
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""" + string.replace(scriptID,'\n','\\n')
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""", version = scriptID)
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)
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parser.add_option('-n','--nodata', dest='data', action='store_false',
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parser.add_option('-n','--nodata', dest='data', action='store_false',
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help='omit microstructure data, just generate mesh')
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help='omit microstructure data, just generate mesh')
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@ -171,7 +151,7 @@ for file in files:
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writer.SetDataModeToBinary()
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writer.SetDataModeToBinary()
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writer.SetCompressorTypeToZLib()
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writer.SetCompressorTypeToZLib()
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writer.SetFileName(os.path.join(dir,'mesh_'+os.path.splitext(file)[0]
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writer.SetFileName(os.path.join(dir,'mesh_'+os.path.splitext(file)[0]
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+'.'+writer.GetDefaultFileExtension()))
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+'.'+writer.GetDefaultFileExtension()))
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if vtk.VTK_MAJOR_VERSION <= 5:
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if vtk.VTK_MAJOR_VERSION <= 5:
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writer.SetInput(grid)
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writer.SetInput(grid)
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else:
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else:
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#!/usr/bin/env python
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#!/usr/bin/env python
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# -*- coding: UTF-8 no BOM -*-
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# -*- coding: UTF-8 no BOM -*-
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import os,sys,string,re,numpy,vtk
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import os,sys,string,re,vtk
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import numpy as np
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import damask
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import damask
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from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
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from optparse import OptionParser
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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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#--------------------------------------------------------------------------------------------------
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# MAIN
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# MAIN
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@ -47,11 +29,10 @@ mappings = {
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}
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}
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parser = OptionParser(option_class=extendedOption, usage='%prog [seedsfile[s]]', description = """
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parser = OptionParser(option_class=damask.extendableOption, usage='%prog [seedsfile[s]]', description = """
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Produce VTK point mesh from seeds file
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Produce VTK point mesh from seeds file
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""" + string.replace(scriptID,'\n','\\n')
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""", version = scriptID)
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)
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parser.add_option('-g', '--grid', dest='grid', type='int', nargs = 3, metavar='int int int', \
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parser.add_option('-g', '--grid', dest='grid', type='int', nargs = 3, metavar='int int int', \
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help='a,b,c grid of hexahedral box [from seeds file]')
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help='a,b,c grid of hexahedral box [from seeds file]')
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@ -90,9 +71,9 @@ for file in files:
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#--- interpret header ----------------------------------------------------------------------------
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#--- interpret header ----------------------------------------------------------------------------
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info = {
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info = {
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'grid': numpy.zeros(3,'i'),
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'grid': np.zeros(3,'i'),
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'size': numpy.zeros(3,'d'),
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'size': np.zeros(3,'d'),
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'origin': numpy.zeros(3,'d'),
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'origin': np.zeros(3,'d'),
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}
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}
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for header in theTable.info:
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for header in theTable.info:
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@ -112,8 +93,8 @@ for file in files:
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'size x y z: %s\n'%(' x '.join(map(str,info['size']))) + \
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'size x y z: %s\n'%(' x '.join(map(str,info['size']))) + \
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'origin x y z: %s\n'%(' : '.join(map(str,info['origin']))))
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'origin x y z: %s\n'%(' : '.join(map(str,info['origin']))))
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if 0 not in options.grid: # user-specified grid
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if 0 not in options.grid: # user-specified grid
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info['grid'] = numpy.array(options.grid)
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info['grid'] = np.array(options.grid)
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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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file['croak'].write('invalid grid a b c.\n')
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# continue
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# continue
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