DAMASK_EICMD/processing/pre/seeds_fromPokes.py

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#!/usr/bin/env python3
import os
import sys
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from io import StringIO
from optparse import OptionParser
import numpy as np
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
Create seeds file by poking at 45 degree through given geom file.
Mimics APS Beamline 34-ID-E DAXM poking.
""", version = scriptID)
parser.add_option('-N', '--points',
dest = 'N',
type = 'int', metavar = 'int',
help = 'number of poking locations [%default]')
parser.add_option('-b', '--box',
dest = 'box',
type = 'float', nargs = 6, metavar = ' '.join(['float']*6),
help = 'bounding box as fraction in x, y, and z directions')
parser.add_option('-x',
action = 'store_true',
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dest = 'x',
help = 'poke 45 deg along x')
parser.add_option('-y',
action = 'store_true',
dest = 'y',
help = 'poke 45 deg along y')
parser.set_defaults(x = False,
y = False,
box = [0.0,1.0,0.0,1.0,0.0,1.0],
N = 16,
)
(options,filenames) = parser.parse_args()
if filenames == []: filenames = [None]
options.box = np.array(options.box).reshape(3,2)
for name in filenames:
damask.util.report(scriptName,name)
geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
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offset =(np.amin(options.box, axis=1)*geom.grid/geom.size).astype(int)
box = np.amax(options.box, axis=1) \
- np.amin(options.box, axis=1)
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Nx = int(options.N/np.sqrt(options.N*geom.size[1]*box[1]/geom.size[0]/box[0]))
Ny = int(options.N/np.sqrt(options.N*geom.size[0]*box[0]/geom.size[1]/box[1]))
Nz = int(box[2]*geom.grid[2])
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damask.util.croak('poking {} x {} x {} in box {} {} {}...'.format(Nx,Ny,Nz,*box))
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seeds = np.zeros((Nx*Ny*Nz,4))
g = np.zeros(3,dtype=np.int)
n = 0
for i in range(Nx):
for j in range(Ny):
g[0] = round((i+0.5)*box[0]*geom.grid[0]/Nx-0.5)+offset[0]
g[1] = round((j+0.5)*box[1]*geom.grid[1]/Ny-0.5)+offset[1]
for k in range(Nz):
g[2] = k + offset[2]
g %= geom.grid
seeds[n,0:3] = (g+0.5)/geom.grid # normalize coordinates to box
seeds[n, 3] = geom.microstructure[g[0],g[1],g[2]]
if options.x: g[0] += 1
if options.y: g[1] += 1
n += 1
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comments = geom.comments \
+ [scriptID + ' ' + ' '.join(sys.argv[1:]),
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'poking\ta {}\tb {}\tc {}'.format(Nx,Ny,Nz),
'grid\ta {}\tb {}\tc {}'.format(*geom.grid),
'size\tx {}\ty {}\tz {}'.format(*geom.size),
'origin\tx {}\ty {}\tz {}'.format(*geom.origin),
'homogenization\t{}'.format(geom.homogenization)]
table = damask.Table(seeds,{'pos':(3,),'microstructure':(1,)},comments)
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table.set('microstructure',table.get('microstructure').astype(np.int))
table.to_ASCII(sys.stdout if name is None else \
os.path.splitext(name)[0]+'_poked_{}.seeds'.format(options.N))