179 lines
6.9 KiB
Python
179 lines
6.9 KiB
Python
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#!/usr/bin/env python
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# -*- coding: UTF-8 no BOM -*-
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import os,sys,string,re,random,math,numpy as np
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import damask
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from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
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scriptID = '$Id$'
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scriptName = scriptID.split()[1]
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# --------------------------------------------------------------------
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# MAIN
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# --------------------------------------------------------------------
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identifiers = {
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'grid': ['a','b','c'],
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'size': ['x','y','z'],
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'origin': ['x','y','z'],
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}
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mappings = {
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'grid': lambda x: int(x),
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'size': lambda x: float(x),
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'origin': lambda x: float(x),
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'homogenization': lambda x: int(x),
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'microstructures': lambda x: int(x),
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}
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parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
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Create seeds file by poking at 45 degree through given geom file.
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Mimics APS Beamline 34-ID-E DAXM poking.
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""", version = scriptID)
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parser.add_option('-N', '--points', dest='N', type='int', metavar='int', \
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help='number of poking locations [%default]')
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parser.add_option('-z', '--planes', dest='z', type='float', nargs = 2, metavar='float float', \
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help='top and bottom z plane')
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parser.add_option('-x', action='store_true', dest='x', \
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help='poke 45 deg along x')
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parser.add_option('-y', action='store_true', dest='y', \
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help='poke 45 deg along y')
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parser.set_defaults(x = False)
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parser.set_defaults(y = False)
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parser.set_defaults(N = 16)
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(options,filenames) = parser.parse_args()
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# --- loop over input files -------------------------------------------------------------------------
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if filenames == []:
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filenames = ['STDIN']
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for name in filenames:
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if name == 'STDIN':
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file = {'name':'STDIN', 'input':sys.stdin, 'output':sys.stdout, 'croak':sys.stderr}
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file['croak'].write('\033[1m'+scriptName+'\033[0m\n')
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else:
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if not os.path.exists(name): continue
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file = {'name':name, 'input':open(name), 'output':open(name+'_tmp','w'), 'croak':sys.stderr}
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file['croak'].write('\033[1m'+scriptName+'\033[0m: '+file['name']+'\n')
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theTable = damask.ASCIItable(file['input'],file['output'],labels = False)
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theTable.head_read()
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#--- interpret header ----------------------------------------------------------------------------
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info = {
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'grid': np.zeros(3,'i'),
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'size': np.zeros(3,'d'),
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'origin': np.zeros(3,'d'),
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'homogenization': 0,
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'microstructures': 0,
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}
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newInfo = {
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'microstructures': 0,
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}
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extra_header = []
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for header in theTable.info:
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headitems = map(str.lower,header.split())
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if len(headitems) == 0: continue
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if headitems[0] in mappings.keys():
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if headitems[0] in identifiers.keys():
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for i in xrange(len(identifiers[headitems[0]])):
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info[headitems[0]][i] = \
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mappings[headitems[0]](headitems[headitems.index(identifiers[headitems[0]][i])+1])
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else:
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info[headitems[0]] = mappings[headitems[0]](headitems[1])
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else:
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extra_header.append(header)
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file['croak'].write('grid a b c: %s\n'%(' x '.join(map(str,info['grid']))) + \
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'size x y z: %s\n'%(' x '.join(map(str,info['size']))) + \
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'origin x y z: %s\n'%(' : '.join(map(str,info['origin']))) + \
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'homogenization: %i\n'%info['homogenization'] + \
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'microstructures: %i\n'%info['microstructures'])
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if np.any(info['grid'] < 1):
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file['croak'].write('invalid grid a b c.\n')
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continue
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if np.any(info['size'] <= 0.0):
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file['croak'].write('invalid size x y z.\n')
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continue
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#--- read data ------------------------------------------------------------------------------------
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microstructure = np.zeros(info['grid'].prod(),'i')
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i = 0
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while theTable.data_read():
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items = theTable.data
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if len(items) > 2:
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if items[1].lower() == 'of': items = [int(items[2])]*int(items[0])
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elif items[1].lower() == 'to': items = xrange(int(items[0]),1+int(items[2]))
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else: items = map(int,items)
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else: items = map(int,items)
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s = len(items)
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microstructure[i:i+s] = items
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i += s
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#--- do work ------------------------------------------------------------------------------------
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Nx = int(options.N/math.sqrt(options.N*info['size'][1]/info['size'][0]))
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Ny = int(options.N/math.sqrt(options.N*info['size'][0]/info['size'][1]))
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Nz = int((max(options.z)-min(options.z))/info['size'][2]*info['grid'][2])
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file['croak'].write('poking %i x %i x %i...\n'%(Nx,Ny,Nz))
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microstructure = microstructure.reshape(info['grid'],order='F')
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seeds = np.zeros((Nx*Ny*Nz,4),'d')
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grid = np.zeros(3,'i')
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offset = min(options.z)/info['size'][2]*info['grid'][2] # offset due to lower z-plane
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n = 0
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for i in xrange(Nx):
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grid[0] = round((i+0.5)*info['grid'][0]/Nx-0.5)
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for j in xrange(Ny):
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grid[1] = round((j+0.5)*info['grid'][1]/Ny-0.5)
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for k in xrange(Nz):
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grid[2] = offset + k
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grid %= info['grid']
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coordinates = (0.5+grid)*info['size']/info['grid']
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seeds[n,0:3] = coordinates/info['size'] # normalize coordinates to box
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seeds[n, 3] = microstructure[grid[0],grid[1],grid[2]]
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# file['croak'].write('%s\t%i\n'%(str(seeds[n,:3]),seeds[n,3]))
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if options.x: grid[0] += 1
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if options.y: grid[1] += 1
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n += 1
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# file['croak'].write('\n')
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newInfo['microstructures'] = len(np.unique(seeds[:,3]))
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#--- report ---------------------------------------------------------------------------------------
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if (newInfo['microstructures'] != info['microstructures']):
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file['croak'].write('--> microstructures: %i\n'%newInfo['microstructures'])
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#--- write header ---------------------------------------------------------------------------------
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theTable.labels_clear()
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theTable.labels_append(['x','y','z','microstructure'])
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theTable.info_clear()
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theTable.info_append(extra_header+[
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scriptID,
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"grid\ta %i\tb %i\tc %i"%(info['grid'][0],info['grid'][1],info['grid'][2],),
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"size\tx %f\ty %f\tz %f"%(info['size'][0],info['size'][1],info['size'][2],),
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"origin\tx %f\ty %f\tz %f"%(info['origin'][0],info['origin'][1],info['origin'][2],),
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"homogenization\t%i"%info['homogenization'],
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"microstructures\t%i"%(newInfo['microstructures']),
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])
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theTable.head_write()
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theTable.output_flush()
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theTable.data = seeds
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theTable.data_writeArray('%g')
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theTable.output_flush()
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#--- output finalization --------------------------------------------------------------------------
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if file['name'] != 'STDIN':
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theTable.close()
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os.rename(file['name']+'_tmp',os.path.splitext(file['name'])[0] + '_poked_%ix%ix%i.seeds'%(Nx,Ny,Nz))
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