using central functionality
This commit is contained in:
Martin Diehl
parent
9dc726ff53
commit
12564557e6
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@ -1,9 +1,12 @@
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#!/usr/bin/env python3
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# -*- coding: UTF-8 no BOM -*-
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import os,sys
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import numpy as np
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import os
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import sys
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from io import StringIO
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from optparse import OptionParser
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import numpy as np
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import damask
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scriptName = os.path.splitext(os.path.basename(__file__))[0]
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@ -29,88 +32,37 @@ parser.add_option('-b',
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action = 'extend', metavar = '<int LIST>',
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dest = 'blacklist',
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help = 'blacklist of grain IDs')
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parser.add_option('-p',
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'--pos', '--seedposition',
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dest = 'pos',
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type = 'string', metavar = 'string',
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help = 'label of coordinates [%default]')
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parser.set_defaults(whitelist = [],
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blacklist = [],
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pos = 'pos',
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)
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(options,filenames) = parser.parse_args()
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options.whitelist = list(map(int,options.whitelist))
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options.blacklist = list(map(int,options.blacklist))
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# --- loop over output files -------------------------------------------------------------------------
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if filenames == []: filenames = [None]
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options.whitelist = [int(i) for i in options.whitelist]
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options.blacklist = [int(i) for i in options.blacklist]
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for name in filenames:
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try: table = damask.ASCIItable(name = name,
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outname = os.path.splitext(name)[0]+'.seeds' if name else name,
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buffered = False,
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labeled = False)
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except: continue
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damask.util.report(scriptName,name)
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# --- interpret header ----------------------------------------------------------------------------
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geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
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microstructure = geom.get_microstructure().reshape((-1,1),order='F')
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table.head_read()
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info,extra_header = table.head_getGeom()
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damask.util.report_geom(info)
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mask = np.logical_and(np.in1d(microstructure,options.whitelist,invert=False) if options.whitelist else \
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np.full(geom.grid.prod(),True,dtype=bool),
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np.in1d(microstructure,options.blacklist,invert=True) if options.blacklist else \
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np.full(geom.grid.prod(),True,dtype=bool))
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errors = []
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if np.any(info['grid'] < 1): errors.append('invalid grid a b c.')
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if np.any(info['size'] <= 0.0): errors.append('invalid size x y z.')
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if errors != []:
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damask.util.croak(errors)
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table.close(dismiss = True)
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continue
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seeds = np.concatenate((damask.grid_filters.cell_coord0(geom.grid,geom.size).reshape((-1,3)),
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microstructure),
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axis=1)[mask]
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# --- read data ------------------------------------------------------------------------------------
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comments = [scriptID + ' ' + ' '.join(sys.argv[1:]),
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"grid\ta {}\tb {}\tc {}".format(*geom.grid),
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"size\tx {}\ty {}\tz {}".format(*geom.size),
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"origin\tx {}\ty {}\tz {}".format(*geom.origin),
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"homogenization\t{}".format(geom.homogenization)]
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microstructure = table.microstructure_read(info['grid']) # read (linear) microstructure
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# --- generate grid --------------------------------------------------------------------------------
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x = (0.5 + np.arange(info['grid'][0],dtype=float))/info['grid'][0]*info['size'][0]+info['origin'][0]
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y = (0.5 + np.arange(info['grid'][1],dtype=float))/info['grid'][1]*info['size'][1]+info['origin'][1]
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z = (0.5 + np.arange(info['grid'][2],dtype=float))/info['grid'][2]*info['size'][2]+info['origin'][2]
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xx = np.tile( x, info['grid'][1]* info['grid'][2])
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yy = np.tile(np.repeat(y,info['grid'][0] ),info['grid'][2])
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zz = np.repeat(z,info['grid'][0]*info['grid'][1])
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mask = np.logical_and(np.in1d(microstructure,options.whitelist,invert=False) if options.whitelist != []
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else np.full_like(microstructure,True,dtype=bool),
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np.in1d(microstructure,options.blacklist,invert=True ) if options.blacklist != []
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else np.full_like(microstructure,True,dtype=bool))
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# ------------------------------------------ assemble header ---------------------------------------
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table.info_clear()
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table.info_append(extra_header+[
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scriptID + ' ' + ' '.join(sys.argv[1:]),
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"grid\ta {}\tb {}\tc {}".format(*info['grid']),
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"size\tx {}\ty {}\tz {}".format(*info['size']),
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"origin\tx {}\ty {}\tz {}".format(*info['origin']),
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"homogenization\t{}".format(info['homogenization']),
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"microstructures\t{}".format(info['microstructures']),
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])
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table.labels_clear()
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table.labels_append(['{dim}_{label}'.format(dim = 1+i,label = options.pos) for i in range(3)]+['microstructure'])
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table.head_write()
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table.output_flush()
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# --- write seeds information ------------------------------------------------------------
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table.data = np.squeeze(np.dstack((xx,yy,zz,microstructure)))[mask]
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table.data_writeArray()
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# ------------------------------------------ finalize output ---------------------------------------
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table.close()
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table = damask.Table(seeds,{'pos':(3,),'microstructure':(1,)},comments)
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table.to_ASCII(sys.stdout if name is None else os.path.splitext(name)[0]+'.seeds')
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