DAMASK_EICMD/processing/pre/geom_addPrimitive.py

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#!/usr/bin/env python3
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import os
import sys
from io import StringIO
from optparse import OptionParser
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import numpy as np
import damask
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scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
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#--------------------------------------------------------------------------------------------------
# MAIN
#--------------------------------------------------------------------------------------------------
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parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [geomfile(s)]', description = """
Inserts a primitive geometric object at a given position.
These objects can be boxes, cylinders, or ellipsoids.
""", version = scriptID)
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parser.add_option('-c', '--center',
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dest='center',
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type='float', nargs = 3, metavar=' '.join(['float']*3),
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help='a,b,c origin of primitive %default')
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parser.add_option('-d', '--dimension',
dest='dimension',
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type='float', nargs = 3, metavar=' '.join(['float']*3),
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help='a,b,c extension of hexahedral box')
parser.add_option('-e', '--exponent',
dest='exponent',
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type='float', nargs = 3, metavar=' '.join(['float']*3),
help='i,j,k exponents for axes: '+
'0 gives octahedron (|x|^(2^0) + |y|^(2^0) + |z|^(2^0) < 1), '+
'1 gives a sphere (|x|^(2^1) + |y|^(2^1) + |z|^(2^1) < 1), '+
'large values produce boxes, negative turn concave.')
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parser.add_option('-f', '--fill',
dest='fill',
type='float', metavar = 'int',
help='microstructure index to fill primitive, defaults to max microstructure index + 1')
parser.add_option('-q', '--quaternion',
dest='quaternion',
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type='float', nargs = 4, metavar=' '.join(['float']*4),
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help = 'rotation of primitive as quaternion')
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parser.add_option('-a', '--angleaxis',
dest='angleaxis',
type=float, nargs = 4, metavar=' '.join(['float']*4),
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help = 'axis and angle to rotate primitive')
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parser.add_option( '--degrees',
dest='degrees',
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action='store_true',
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help = 'angle is given in degrees')
parser.add_option( '--nonperiodic',
dest='periodic',
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action='store_false',
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help = 'wrap around edges')
parser.add_option( '--realspace',
dest='realspace',
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action='store_true',
help = '-c and -d span [origin,origin+size] instead of [0,grid] coordinates')
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parser.add_option( '--invert',
dest='inside',
action='store_false',
help = 'invert the volume filled by the primitive (inside/outside)')
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parser.set_defaults(center = (.0,.0,.0),
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degrees = False,
exponent = (20,20,20), # box shape by default
periodic = True,
realspace = False,
inside = True,
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)
(options, filenames) = parser.parse_args()
if options.dimension is None:
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parser.error('no dimension specified.')
if [options.angleaxis,options.quaternion].count(None) == 0:
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parser.error('more than one rotation specified.')
if options.angleaxis is not None:
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rotation = damask.Rotation.fromAxisAngle(np.array(options.angleaxis),options.degrees,normalise=True)
elif options.quaternion is not None:
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rotation = damask.Rotation.fromQuaternion(options.quaternion)
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else:
rotation = damask.Rotation()
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if filenames == []: filenames = [None]
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for name in filenames:
damask.util.report(scriptName,name)
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geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
grid = geom.get_grid()
size = geom.get_size()
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# scale to box of size [1.0,1.0,1.0]
if options.realspace:
center = (np.array(options.center) - geom.get_origin())/size
r = np.array(options.dimension)/size/2.0
else:
center = (np.array(options.center) + 0.5)/grid
r = np.array(options.dimension)/grid/2.0
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if np.any(center<0.0) or np.any(center>=1.0): print('error')
offset = np.ones(3)*0.5 if options.periodic else center
mask = np.full(grid,False)
# High exponents can cause underflow & overflow - okay here, just compare to 1, so +infinity and 0 are fine
np.seterr(over='ignore', under='ignore')
e = 2.0**np.array(options.exponent)
for x in range(grid[0]):
for y in range(grid[1]):
for z in range(grid[2]):
coords = np.array([x+0.5,y+0.5,z+0.5])/grid
mask[x,y,z] = np.sum(np.abs((rotation*(coords-offset))/r)**e) < 1
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if options.periodic:
shift = ((offset-center)*grid).astype(int)
mask = np.roll(mask,shift,(0,1,2))
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if options.inside: mask = np.logical_not(mask)
fill = np.nanmax(geom.microstructure)+1 if options.fill is None else options.fill
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damask.util.croak(geom.update(np.where(mask,geom.microstructure,fill)))
geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
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if name is None:
sys.stdout.write(str(geom.show()))
else:
geom.to_file(name)