#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
import os,sys,string,re,random,math,numpy as np
import damask
from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
scriptID = '$Id$'
scriptName = scriptID.split()[1]
# --------------------------------------------------------------------
# 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 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('-z', '--planes', dest='z', type='float', nargs = 2, metavar='float float', \
help='top and bottom z plane')
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.set_defaults(x = False)
parser.set_defaults(y = False)
parser.set_defaults(N = 16)
(options,filenames) = parser.parse_args()
# --- loop over input files -------------------------------------------------------------------------
if filenames == []:
filenames = ['STDIN']
for name in filenames:
if name == 'STDIN':
file = {'name':'STDIN', 'input':sys.stdin, 'output':sys.stdout, 'croak':sys.stderr}
file['croak'].write('\033[1m'+scriptName+'\033[0m\n')
else:
if not os.path.exists(name): continue
file = {'name':name, 'input':open(name), 'output':open(name+'_tmp','w'), 'croak':sys.stderr}
file['croak'].write('\033[1m'+scriptName+'\033[0m: '+file['name']+'\n')
theTable = damask.ASCIItable(file['input'],file['output'],labels = False)
theTable.head_read()
#--- interpret header ----------------------------------------------------------------------------
info = {
'grid': np.zeros(3,'i'),
'size': np.zeros(3,'d'),
'origin': np.zeros(3,'d'),
'homogenization': 0,
'microstructures': 0,
}
newInfo = {
'microstructures': 0,
}
extra_header = []
for header in theTable.info:
headitems = map(str.lower,header.split())
if len(headitems) == 0: continue
if headitems[0] in mappings.keys():
if headitems[0] in identifiers.keys():
for i in xrange(len(identifiers[headitems[0]])):
info[headitems[0]][i] = \
mappings[headitems[0]](headitems[headitems.index(identifiers[headitems[0]][i])+1])
else:
info[headitems[0]] = mappings[headitems[0]](headitems[1])
else:
extra_header.append(header)
file['croak'].write('grid a b c: %s\n'%(' x '.join(map(str,info['grid']))) + \
'size x y z: %s\n'%(' x '.join(map(str,info['size']))) + \
'origin x y z: %s\n'%(' : '.join(map(str,info['origin']))) + \
'homogenization: %i\n'%info['homogenization'] + \
'microstructures: %i\n'%info['microstructures'])
if np.any(info['grid'] < 1):
file['croak'].write('invalid grid a b c.\n')
continue
if np.any(info['size'] <= 0.0):
file['croak'].write('invalid size x y z.\n')
continue
#--- read data ------------------------------------------------------------------------------------
microstructure = np.zeros(info['grid'].prod(),'i')
i = 0
while theTable.data_read():
items = theTable.data
if len(items) > 2:
if items[1].lower() == 'of': items = [int(items[2])]*int(items[0])
elif items[1].lower() == 'to': items = xrange(int(items[0]),1+int(items[2]))
else: items = map(int,items)
else: items = map(int,items)
s = len(items)
microstructure[i:i+s] = items
i += s
#--- do work ------------------------------------------------------------------------------------
Nx = int(options.N/math.sqrt(options.N*info['size'][1]/info['size'][0]))
Ny = int(options.N/math.sqrt(options.N*info['size'][0]/info['size'][1]))
Nz = int((max(options.z)-min(options.z))/info['size'][2]*info['grid'][2])
file['croak'].write('poking %i x %i x %i...\n'%(Nx,Ny,Nz))
microstructure = microstructure.reshape(info['grid'],order='F')
seeds = np.zeros((Nx*Ny*Nz,4),'d')
grid = np.zeros(3,'i')
offset = min(options.z)/info['size'][2]*info['grid'][2] # offset due to lower z-plane
n = 0
for i in xrange(Nx):
grid[0] = round((i+0.5)*info['grid'][0]/Nx-0.5)
for j in xrange(Ny):
grid[1] = round((j+0.5)*info['grid'][1]/Ny-0.5)
for k in xrange(Nz):
grid[2] = offset + k
grid %= info['grid']
coordinates = (0.5+grid)*info['size']/info['grid']
seeds[n,0:3] = coordinates/info['size'] # normalize coordinates to box
seeds[n, 3] = microstructure[grid[0],grid[1],grid[2]]
# file['croak'].write('%s\t%i\n'%(str(seeds[n,:3]),seeds[n,3]))
if options.x: grid[0] += 1
if options.y: grid[1] += 1
n += 1
# file['croak'].write('\n')
newInfo['microstructures'] = len(np.unique(seeds[:,3]))
#--- report ---------------------------------------------------------------------------------------
if (newInfo['microstructures'] != info['microstructures']):
file['croak'].write('--> microstructures: %i\n'%newInfo['microstructures'])
#--- write header ---------------------------------------------------------------------------------
theTable.labels_clear()
theTable.labels_append(['x','y','z','microstructure'])
theTable.info_clear()
theTable.info_append(extra_header+[
scriptID,
"grid\ta %i\tb %i\tc %i"%(info['grid'][0],info['grid'][1],info['grid'][2],),
"size\tx %f\ty %f\tz %f"%(info['size'][0],info['size'][1],info['size'][2],),
"origin\tx %f\ty %f\tz %f"%(info['origin'][0],info['origin'][1],info['origin'][2],),
"homogenization\t%i"%info['homogenization'],
"microstructures\t%i"%(newInfo['microstructures']),
])
theTable.head_write()
theTable.output_flush()
theTable.data = seeds
theTable.data_writeArray('%g')
theTable.output_flush()
#--- output finalization --------------------------------------------------------------------------
if file['name'] != 'STDIN':
theTable.close()
os.rename(file['name']+'_tmp',os.path.splitext(file['name'])[0] + '_poked_%ix%ix%i.seeds'%(Nx,Ny,Nz))