DAMASK_EICMD/processing/pre/geom_addPrimitive.py

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#!/usr/bin/env python3
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# -*- coding: UTF-8 no BOM -*-
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import os,sys,math
import numpy as np
from optparse import OptionParser
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import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
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#--------------------------------------------------------------------------------------------------
# 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),
}
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parser = OptionParser(option_class=damask.extendableOption, usage='%prog option [geomfile(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('-c', '--center', dest='center',
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',
type='float', nargs = 3, metavar=' '.join(['float']*3),
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help='a,b,c extension of hexahedral box; negative values are diameters')
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parser.add_option('-e', '--exponent', dest='exponent',
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 turns concave.')
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parser.add_option('-f', '--fill', dest='fill',
type='float', metavar = 'float',
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help='grain index to fill primitive. "0" selects maximum microstructure index + 1 [%default]')
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parser.add_option('-q', '--quaternion', dest='quaternion',
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),
help = 'axis and angle to rotate primitive')
parser.add_option( '--degrees', dest='degrees',
action='store_true',
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help = 'angle is given in degrees [%default]')
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parser.add_option( '--nonperiodic', dest='periodic',
action='store_false',
help = 'wrap around edges [%default]')
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parser.add_option( '--realspace', dest='realspace',
action='store_true',
help = '-c and -d span [origin,origin+size] instead of [0,grid] coordinates')
parser.add_option( '--invert', dest='inside',
action='store_false',
help = 'invert the volume filled by the primitive (inside/outside)')
parser.add_option('--float', dest = 'float',
action = 'store_true',
help = 'use float input')
parser.set_defaults(center = (.0,.0,.0),
fill = 0.0,
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degrees = False,
exponent = (20,20,20), # box shape by default
periodic = True,
realspace = False,
inside = True,
float = False,
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)
(options, filenames) = parser.parse_args()
if options.dimension is None:
parser.error('no dimension 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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datatype = 'f' if options.float else 'i'
options.center = np.array(options.center)
options.dimension = np.array(options.dimension)
# undo logarithmic sense of exponent and generate ellipsoids for negative dimensions (backward compatibility)
options.exponent = np.where(np.array(options.dimension) > 0, np.power(2,options.exponent), 2)
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# --- loop over input files -------------------------------------------------------------------------
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if filenames == []: filenames = [None]
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for name in filenames:
try: table = damask.ASCIItable(name = name,
buffered = False,
labeled = False)
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except: continue
damask.util.report(scriptName,name)
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# --- interpret header ----------------------------------------------------------------------------
table.head_read()
info,extra_header = table.head_getGeom()
damask.util.report_geom(info)
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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 != []:
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damask.util.croak(errors)
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table.close(dismiss = True)
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continue
#--- read data ------------------------------------------------------------------------------------
microstructure = table.microstructure_read(info['grid'],datatype) # read microstructure
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# --- do work ------------------------------------------------------------------------------------
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newInfo = {
'microstructures': 0,
}
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options.fill = np.nanmax(microstructure)+1 if options.fill == 0 else options.fill
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microstructure = microstructure.reshape(info['grid'],order='F')
# coordinates given in real space (default) vs voxel space
if options.realspace:
options.center -= info['origin']
options.center *= np.array(info['grid']) / np.array(info['size'])
options.dimension *= np.array(info['grid']) / np.array(info['size'])
grid = 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(-grid[0]/2, (3*grid[0])/2, dtype=np.float32), # 50% padding on each side
np.arange(-grid[1]/2, (3*grid[1])/2, dtype=np.float32),
np.arange(-grid[2]/2, (3*grid[2])/2, dtype=np.float32),
indexing='ij')
# Padding handling
X = np.roll(np.roll(np.roll(X,
-grid[0]//2, axis=0),
-grid[1]//2, axis=1),
-grid[2]//2, axis=2)
Y = np.roll(np.roll(np.roll(Y,
-grid[0]//2, axis=0),
-grid[1]//2, axis=1),
-grid[2]//2, axis=2)
Z = np.roll(np.roll(np.roll(Z,
-grid[0]//2, axis=0),
-grid[1]//2, axis=1),
-grid[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, grid[0], dtype=np.float32),
np.arange(0, grid[1], dtype=np.float32),
np.arange(0, grid[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 rotation
(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(grid, 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[grid[0] * i : grid[0] * (i+1),
grid[1] * j : grid[1] * (j+1),
grid[2] * k : grid[2] * (k+1)])**options.exponent[0] +
np.abs(Y[grid[0] * i : grid[0] * (i+1),
grid[1] * j : grid[1] * (j+1),
grid[2] * k : grid[2] * (k+1)])**options.exponent[1] +
np.abs(Z[grid[0] * i : grid[0] * (i+1),
grid[1] * j : grid[1] * (j+1),
grid[2] * k : grid[2] * (k+1)])**options.exponent[2] <= 1.0)
microstructure = np.where(inside,
options.fill if options.inside else microstructure,
microstructure if options.inside else options.fill)
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] <= 1.0,
options.fill if options.inside else microstructure,
microstructure if options.inside else options.fill)
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np.seterr(**old_settings) # Reset warnings to old state
newInfo['microstructures'] = len(np.unique(microstructure))
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# --- report ---------------------------------------------------------------------------------------
if (newInfo['microstructures'] != info['microstructures']):
damask.util.croak('--> microstructures: {}'.format(newInfo['microstructures']))
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#--- write header ---------------------------------------------------------------------------------
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table.info_clear()
table.info_append(extra_header+[
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scriptID + ' ' + ' '.join(sys.argv[1:]),
"grid\ta {}\tb {}\tc {}".format(*info['grid']),
"size\tx {}\ty {}\tz {}".format(*info['size']),
"origin\tx {}\ty {}\tz {}".format(*info['origin']),
"homogenization\t{}".format(info['homogenization']),
"microstructures\t{}".format(newInfo['microstructures']),
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])
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table.labels_clear()
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table.head_write()
table.output_flush()
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# --- write microstructure information ------------------------------------------------------------
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format = '%g' if options.float else '%{}i'.format(int(math.floor(math.log10(np.nanmax(microstructure))+1)))
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table.data = microstructure.reshape((info['grid'][0],info['grid'][1]*info['grid'][2]),order='F').transpose()
table.data_writeArray(format,delimiter = ' ')
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#--- output finalization --------------------------------------------------------------------------
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table.close()