#!/usr/bin/env python2.7
# -*- coding: UTF-8 no BOM -*-
import os,sys,math
import numpy as np
from optparse import OptionParser
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
#--------------------------------------------------------------------------------------------------
# MAIN
#--------------------------------------------------------------------------------------------------
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 option(s) [geomfile(s)]', 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.
""", version = scriptID)
parser.add_option('-c', '--center', dest='center', type='float', nargs = 3, metavar=' '.join(['float']*3),
help='a,b,c origin of primitive %default')
parser.add_option('-d', '--dimension', dest='dimension', type='float', nargs = 3, metavar=' '.join(['float']*3),
help='a,b,c extension of hexahedral box; negative values are diameters')
parser.add_option('-e', '--exponent', dest='exponent', type='float', nargs = 3, metavar=' '.join(['float']*3),
help='i,j,k exponents for axes - 2 gives a sphere (x^2 + y^2 + z^2 < 1), 1 makes \
octahedron (|x| + |y| + |z| < 1). Large values produce boxes, 0 - 1 is concave. ')
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),
help = 'angle,x,y,z clockwise rotation of primitive about axis by angle')
parser.add_option( '--degrees', dest='degrees', action='store_true',
help = 'angle is given in degrees [%default]')
parser.add_option( '--nonperiodic', dest='periodic', action='store_false',
help = 'wrap around edges [%default]')
parser.add_option( '--voxelspace', dest='voxelspace', action='store_true',
help = '-c and -d are given in (0 to grid) coordinates instead of (origin to origin+size) \
coordinates [%default]')
parser.set_defaults(center = (.0,.0,.0),
fill = 0,
degrees = False,
exponent = (1e10,1e10,1e10), # box shape by default
periodic = True,
voxelspace = False
)
(options, filenames) = parser.parse_args()
if options.dimension is None:
parser.error('no dimension specified.')
if options.angleaxis is not None:
options.angleaxis = map(float,options.angleaxis)
rotation = damask.Quaternion().fromAngleAxis(np.radians(options.angleaxis[0]) if options.degrees else options.angleaxis[0],
options.angleaxis[1:4])
elif options.quaternion is not None:
options.quaternion = map(float,options.quaternion)
rotation = damask.Quaternion(options.quaternion)
else:
rotation = damask.Quaternion()
options.center = np.array(options.center)
options.dimension = np.array(options.dimension)
# --- loop over input files -------------------------------------------------------------------------
if filenames == []: filenames = [None]
for name in filenames:
try:
table = damask.ASCIItable(name = name,
buffered = False, labeled = False)
except: continue
damask.util.report(scriptName,name)
# --- interpret header ----------------------------------------------------------------------------
table.head_read()
info,extra_header = table.head_getGeom()
damask.util.croak(['grid a b c: %s'%(' x '.join(map(str,info['grid']))),
'size x y z: %s'%(' x '.join(map(str,info['size']))),
'origin x y z: %s'%(' : '.join(map(str,info['origin']))),
'homogenization: %i'%info['homogenization'],
'microstructures: %i'%info['microstructures'],
])
errors = []
if np.any(info['grid'] < 1): errors.append('invalid grid a b c.')
if np.any(info['size'] <= 0.0): errors.append('invalid size x y z.')
if errors != []:
damask.util.croak(errors)
table.close(dismiss = True)
continue
#--- read data ------------------------------------------------------------------------------------
microstructure = table.microstructure_read(info['grid']) # read microstructure
# --- do work ------------------------------------------------------------------------------------
newInfo = {
'microstructures': 0,
}
if options.fill == 0:
options.fill = microstructure.max()+1
# If we have a negative dimension, make it an ellipsoid for backwards compatibility
options.exponent = np.where(np.array(options.dimension) > 0, options.exponent, 2)
microstructure = microstructure.reshape(info['grid'],order='F')
# coordinates given in real space (default) vs voxel space
if not options.voxelspace:
options.center += info['origin']
options.center *= np.array(info['grid']) / np.array(info['size'])
options.dimension *= np.array(info['grid']) / np.array(info['size'])
size = microstructure.shape
# change to coordinate space where the primitive is the unit sphere/cube/etc
if options.periodic: # use padding to achieve periodicity
(X, Y, Z) = np.meshgrid(np.arange(-size[0]/2, (3*size[0])/2, dtype=np.float32), # 50% padding on each side
np.arange(-size[1]/2, (3*size[1])/2, dtype=np.float32),
np.arange(-size[2]/2, (3*size[2])/2, dtype=np.float32),
indexing='ij')
# Padding handling
X = np.roll(np.roll(np.roll(X,
-size[0]/2, axis=0),
-size[1]/2, axis=1),
-size[2]/2, axis=2)
Y = np.roll(np.roll(np.roll(Y,
-size[0]/2, axis=0),
-size[1]/2, axis=1),
-size[2]/2, axis=2)
Z = np.roll(np.roll(np.roll(Z,
-size[0]/2, axis=0),
-size[1]/2, axis=1),
-size[2]/2, axis=2)
else: # nonperiodic, much lighter on resources
# change to coordinate space where the primitive is the unit sphere/cube/etc
(X, Y, Z) = np.meshgrid(np.arange(0, size[0], dtype=np.float32),
np.arange(0, size[1], dtype=np.float32),
np.arange(0, size[2], dtype=np.float32),
indexing='ij')
# first by translating the center onto 0, 0.5 shifts the voxel origin onto the center of the voxel
X -= options.center[0] - 0.5
Y -= options.center[1] - 0.5
Z -= options.center[2] - 0.5
# and then by applying the quaternion
# this should be rotation.conjugate() * (X,Y,Z), but it is this way for backwards compatibility with the older version of this script
(X, Y, Z) = rotation * (X, Y, Z)
# and finally by scaling (we don't worry about options.dimension being negative, np.abs occurs on the microstructure = np.where... line)
X /= options.dimension[0] * 0.5
Y /= options.dimension[1] * 0.5
Z /= options.dimension[2] * 0.5
# High exponents can cause underflow & overflow - loss of precision is okay here, we just compare it to 1, so +infinity and 0 are fine
old_settings = np.seterr()
np.seterr(over='ignore', under='ignore')
if options.periodic: # use padding to achieve periodicity
inside = np.zeros(size, dtype=bool)
for i in range(2):
for j in range(2):
for k in range(2):
inside = inside | ( # Most of this is handling the padding
np.abs(X[size[0] * i : size[0] * (i+1),
size[1] * j : size[1] * (j+1),
size[2] * k : size[2] * (k+1)])**options.exponent[0] +
np.abs(Y[size[0] * i : size[0] * (i+1),
size[1] * j : size[1] * (j+1),
size[2] * k : size[2] * (k+1)])**options.exponent[1] +
np.abs(Z[size[0] * i : size[0] * (i+1),
size[1] * j : size[1] * (j+1),
size[2] * k : size[2] * (k+1)])**options.exponent[2] < 1)
microstructure = np.where(inside, options.fill, microstructure)
else: # nonperiodic, much lighter on resources
microstructure = np.where(np.abs(X)**options.exponent[0] +
np.abs(Y)**options.exponent[1] +
np.abs(Z)**options.exponent[2] < 1, options.fill, microstructure)
np.seterr(**old_settings) # Reset warnings to old state
newInfo['microstructures'] = microstructure.max()
# --- report ---------------------------------------------------------------------------------------
if (newInfo['microstructures'] != info['microstructures']):
damask.util.croak('--> microstructures: %i'%newInfo['microstructures'])
#--- write header ---------------------------------------------------------------------------------
table.info_clear()
table.info_append([
scriptID + ' ' + ' '.join(sys.argv[1:]),
"grid\ta {grid[0]}\tb {grid[1]}\tc {grid[2]}".format(grid=info['grid']),
"size\tx {size[0]}\ty {size[1]}\tz {size[2]}".format(size=info['size']),
"origin\tx {origin[0]}\ty {origin[1]}\tz {origin[2]}".format(origin=info['origin']),
"homogenization\t{homog}".format(homog=info['homogenization']),
"microstructures\t{microstructures}".format(microstructures=newInfo['microstructures']),
extra_header
])
table.labels_clear()
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 --------------------------------------------------------------------------
table.close()