DAMASK_EICMD/processing/pre/seeds_fromPokes.py

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#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
import os,math,sys
import numpy as np
import damask
from optparse import OptionParser
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',
dest = 'x',
help = 'poke 45 deg along x')
parser.add_option('-y',
action = 'store_true',
dest = 'y',
help = 'poke 45 deg along y')
parser.add_option('-p','--position',
dest = 'position',
type = 'string', metavar = 'string',
help = 'column label for coordinates [%default]')
parser.set_defaults(x = False,
y = False,
box = [0.0,1.0,0.0,1.0,0.0,1.0],
N = 16,
position = 'pos',
)
(options,filenames) = parser.parse_args()
options.box = np.array(options.box).reshape(3,2)
# --- loop over output files -------------------------------------------------------------------------
if filenames == []: filenames = [None]
for name in filenames:
try:
table = damask.ASCIItable(name = name,
outname = os.path.splitext(name)[-2]+'_poked_{}.seeds'.format(options.N) if name else 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']))),
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'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']).reshape(info['grid'],order='F') # read microstructure
# --- do work ------------------------------------------------------------------------------------
newInfo = {
'microstructures': 0,
}
offset = (np.amin(options.box, axis=1)*info['grid']/info['size']).astype(int)
box = np.amax(options.box, axis=1) - np.amin(options.box, axis=1)
Nx = int(options.N/math.sqrt(options.N*info['size'][1]*box[1]/info['size'][0]/box[0]))
Ny = int(options.N/math.sqrt(options.N*info['size'][0]*box[0]/info['size'][1]/box[1]))
Nz = int(box[2]*info['grid'][2])
damask.util.croak('poking {} x {} x {} in box {} {} {}...'.format(Nx,Ny,Nz,*box))
seeds = np.zeros((Nx*Ny*Nz,4),'d')
grid = np.zeros(3,'i')
n = 0
for i in xrange(Nx):
for j in xrange(Ny):
grid[0] = round((i+0.5)*box[0]*info['grid'][0]/Nx-0.5)+offset[0]
grid[1] = round((j+0.5)*box[1]*info['grid'][1]/Ny-0.5)+offset[1]
damask.util.croak('x,y coord on surface: {},{}...'.format(*grid[:2]))
for k in xrange(Nz):
grid[2] = k + offset[2]
grid %= info['grid']
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seeds[n,0:3] = (0.5+grid)/info['grid'] # normalize coordinates to box
seeds[n, 3] = microstructure[grid[0],grid[1],grid[2]]
if options.x: grid[0] += 1
if options.y: grid[1] += 1
n += 1
newInfo['microstructures'] = len(np.unique(seeds[:,3]))
# --- report ---------------------------------------------------------------------------------------
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if (newInfo['microstructures'] != info['microstructures']):
damask.util.croak(remarks.append('--> microstructures: %i'%newInfo['microstructures']))
# ------------------------------------------ assemble header ---------------------------------------
table.info_clear()
table.info_append(extra_header+[
scriptID + ' ' + ' '.join(sys.argv[1:]),
"poking\ta {}\tb {}\tc {}".format(Nx,Ny,Nz),
"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']),
])
table.labels_clear()
table.labels_append(['{dim}_{label}'.format(dim = 1+i,label = options.position) for i in range(3)]+['microstructure'])
table.head_write()
table.output_flush()
# --- write seeds information ------------------------------------------------------------
table.data = seeds
table.data_writeArray()
# --- output finalization --------------------------------------------------------------------------
table.close() # close ASCII table