Create seeds file by poking at 45 degree through given geom file.
Mimics APS Beamline 34-ID-E DAXM poking.
This commit is contained in:
Philip Eisenlohr
parent
6eb83530b8
commit
f50927b99f
|
|
@ -0,0 +1,178 @@
|
|||
#!/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))
|
||||
Loading…
Reference in New Issue