DAMASK_EICMD/processing/pre/geom_addPrimitive.py

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#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
import os,re,sys,math,string
import numpy as np
from optparse import OptionParser
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import damask
scriptID = string.replace('$Id: geom_pack.py 3679 2014-11-05 22:01:11Z p.eisenlohr $','\n','\\n')
scriptName = scriptID.split()[1][:-3]
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oversampling = 2.
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#--------------------------------------------------------------------------------------------------
# MAIN
#--------------------------------------------------------------------------------------------------
synonyms = {
'grid': ['resolution'],
'size': ['dimension'],
}
identifiers = {
'grid': ['a','b','c'],
'size': ['x','y','z'],
'origin': ['x','y','z'],
}
mappings = {
'grid': lambda x: int(x),
'size': lambda x: float(x),
'origin': lambda x: float(x),
'homogenization': lambda x: int(x),
'microstructures': lambda x: int(x),
}
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.
Depending on the sign of the dimension parameters, these objects can be boxes, cylinders, or ellipsoids.
""", version = scriptID)
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parser.add_option('-o', '--origin',
'-c', '--center', dest='center', type='int', nargs = 3, metavar=' '.join(['int']*3),
help='a,b,c origin of primitive %default')
parser.add_option('-d', '--dimension', dest='dimension', type='int', nargs = 3, metavar=' '.join(['int']*3),
help='a,b,c extension of hexahedral box; negative values are diameters')
parser.add_option('-f', '--fill', dest='fill', type='int', metavar = 'int',
help='grain index to fill primitive. "0" selects maximum microstructure index + 1 [%default]')
parser.add_option('-q', '--quaternion', dest='quaternion', type='float', nargs = 4, metavar=' '.join(['float']*4),
help = 'rotation of primitive as quaternion')
parser.add_option('-a', '--angleaxis', dest='angleaxis', nargs = 4, metavar=' '.join(['float']*4),
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help = 'rotation of primitive as angle and axis')
parser.add_option( '--degrees', dest='degrees', action='store_true',
help = 'angle is given in degrees [%default]')
parser.set_defaults(center = [0,0,0],
fill = 0,
quaternion = [],
angleaxis = [],
degrees = False,
)
(options, filenames) = parser.parse_args()
if options.angleaxis != []:
options.angleaxis = map(float,options.angleaxis)
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()
elif options.quaternion != []:
options.rotation = map(float,options.rotation)
rotation = damask.Quaternion(options.quaternion).conjugated()
else:
rotation = damask.Quaternion().conjugated()
options.center = np.array(options.center)
invRotation = rotation.conjugated() # rotation of gridpos into primitive coordinate system
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#--- setup file handles --------------------------------------------------------------------------
files = []
if filenames == []:
files.append({'name':'STDIN',
'input':sys.stdin,
'output':sys.stdout,
'croak':sys.stderr,
})
else:
for name in filenames:
if os.path.exists(name):
files.append({'name':name,
'input':open(name),
'output':open(name+'_tmp','w'),
'croak':sys.stdout,
})
#--- loop over input files ------------------------------------------------------------------------
for file in files:
if file['name'] != 'STDIN': file['croak'].write('\033[1m'+scriptName+'\033[0m: '+file['name']+'\n')
else: file['croak'].write('\033[1m'+scriptName+'\033[0m\n')
table = damask.ASCIItable(file['input'],file['output'],labels = False)
table.head_read()
#--- interpret header ----------------------------------------------------------------------------
info = {
'grid': np.zeros(3,'i'),
'size': np.zeros(3,'d'),
'origin': np.zeros(3,'d'),
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'homogenization': 0,
'microstructures': 0,
}
newInfo = {
'grid': np.zeros(3,'i'),
'origin': np.zeros(3,'d'),
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'microstructures': 0,
}
extra_header = []
for header in table.info:
headitems = map(str.lower,header.split())
if len(headitems) == 0: continue # skip blank lines
for synonym,alternatives in synonyms.iteritems():
if headitems[0] in alternatives: headitems[0] = synonym
if headitems[0] in mappings.keys():
if headitems[0] in identifiers.keys():
for i in xrange(len(identifiers[headitems[0]])):
info[headitems[0]][i] = \
mappings[headitems[0]](headitems[headitems.index(identifiers[headitems[0]][i])+1])
else:
info[headitems[0]] = mappings[headitems[0]](headitems[1])
else:
extra_header.append(header)
file['croak'].write('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'])
if np.any(info['grid'] < 1):
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file['croak'].write('invalid grid a b c.\n')
continue
if np.any(info['size'] <= 0.0):
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file['croak'].write('invalid size x y z.\n')
continue
#--- read data ------------------------------------------------------------------------------------
microstructure = np.zeros(info['grid'].prod(),'i') # initialize as flat array
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i = 0
while table.data_read():
items = table.data
if len(items) > 2:
if items[1].lower() == 'of': items = [int(items[2])]*int(items[0])
elif items[1].lower() == 'to': items = xrange(int(items[0]),1+int(items[2]))
else: items = map(int,items)
else: items = map(int,items)
s = len(items)
microstructure[i:i+s] = items
i += s
#--- do work ------------------------------------------------------------------------------------
if options.fill == 0:
options.fill = microstructure.max()+1
microstructure = microstructure.reshape(info['grid'],order='F')
if options.dimension != None:
mask = (np.array(options.dimension) < 0).astype(float) # zero where positive dimension, otherwise one
dim = abs(np.array(options.dimension)) # dimensions of primitive body
pos = np.zeros(3,dtype='float')
# 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(np.arange(-dim[0]/oversampling,(dim[0]+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(np.arange(-dim[2]/oversampling,(dim[2]+1)/oversampling,1./oversampling)):
gridpos = np.floor(rotation*pos) # rotate and lock into spacial grid
primPos = invRotation*gridpos # rotate back to primitive coordinate system
if np.dot(mask*primPos/dim,mask*primPos/dim) <= 0.25 and \
np.all(abs((1.-mask)*primPos/dim) <= 0.5): # inside ellipsoid and inside box
microstructure[(gridpos[0]+options.center[0])%info['grid'][0],
(gridpos[1]+options.center[1])%info['grid'][1],
(gridpos[2]+options.center[2])%info['grid'][2]] = options.fill # assign microstructure index
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newInfo['microstructures'] = microstructure.max()
#--- report ---------------------------------------------------------------------------------------
if (newInfo['microstructures'] != info['microstructures']):
file['croak'].write('--> microstructures: %i\n'%newInfo['microstructures'])
#--- write header ---------------------------------------------------------------------------------
table.labels_clear()
table.info_clear()
table.info_append(extra_header+[
scriptID + ' ' + ' '.join(sys.argv[1:]),
"grid\ta %i\tb %i\tc %i"%(info['grid'][0],info['grid'][1],info['grid'][2],),
"size\tx %f\ty %f\tz %f"%(info['size'][0],info['size'][1],info['size'][2],),
"origin\tx %f\ty %f\tz %f"%(info['origin'][0],info['origin'][1],info['origin'][2],),
"homogenization\t%i"%info['homogenization'],
"microstructures\t%i"%(newInfo['microstructures']),
])
table.head_write()
table.output_flush()
# --- write microstructure information ------------------------------------------------------------
formatwidth = int(math.floor(math.log10(microstructure.max())+1))
table.data = microstructure.reshape((info['grid'][0],info['grid'][1]*info['grid'][2]),order='F').transpose()
table.data_writeArray('%%%ii'%(formatwidth),delimiter=' ')
#--- output finalization --------------------------------------------------------------------------
if file['name'] != 'STDIN':
table.input_close()
table.output_close()
os.rename(file['name']+'_tmp',file['name'])