same functionality can be accomplished with existing scripts.
addEuclideanDistance + geom_fromTable (reLabel) + specify grid and size
This commit is contained in:
Philip Eisenlohr
parent
2daa162da2
commit
db7c4bba45
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@ -1,219 +0,0 @@
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#!/usr/bin/env python
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# -*- coding: UTF-8 no BOM -*-
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import os,sys,math,itertools
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import numpy as np
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from scipy import ndimage
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from optparse import OptionParser
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import damask
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scriptName = os.path.splitext(os.path.basename(__file__))[0]
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scriptID = ' '.join([scriptName,damask.version])
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def periodic_3Dpad(array, rimdim=(1,1,1)):
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rimdim = np.array(rimdim,'i')
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size = np.array(array.shape,'i')
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padded = np.empty(size+2*rimdim,array.dtype)
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padded[rimdim[0]:rimdim[0]+size[0],
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rimdim[1]:rimdim[1]+size[1],
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rimdim[2]:rimdim[2]+size[2]] = array
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p = np.zeros(3,'i')
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for side in xrange(3):
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for p[(side+2)%3] in xrange(padded.shape[(side+2)%3]):
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for p[(side+1)%3] in xrange(padded.shape[(side+1)%3]):
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for p[side%3] in xrange(rimdim[side%3]):
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spot = (p-rimdim)%size
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padded[p[0],p[1],p[2]] = array[spot[0],spot[1],spot[2]]
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for p[side%3] in xrange(rimdim[side%3]+size[side%3],size[side%3]+2*rimdim[side%3]):
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spot = (p-rimdim)%size
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padded[p[0],p[1],p[2]] = array[spot[0],spot[1],spot[2]]
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return padded
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#--------------------------------------------------------------------------------------------------
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# MAIN
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#--------------------------------------------------------------------------------------------------
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features = [
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{'aliens': 1, 'alias': ['boundary','biplane'],},
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{'aliens': 2, 'alias': ['tripleline',],},
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{'aliens': 3, 'alias': ['quadruplepoint',],}
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]
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neighborhoods = {
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'neumann':np.array([
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[-1, 0, 0],
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[ 1, 0, 0],
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[ 0,-1, 0],
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[ 0, 1, 0],
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[ 0, 0,-1],
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[ 0, 0, 1],
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]),
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'moore':np.array([
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[-1,-1,-1],
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[ 0,-1,-1],
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[ 1,-1,-1],
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[-1, 0,-1],
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[ 0, 0,-1],
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[ 1, 0,-1],
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[-1, 1,-1],
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[ 0, 1,-1],
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[ 1, 1,-1],
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#
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[-1,-1, 0],
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[ 0,-1, 0],
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[ 1,-1, 0],
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[-1, 0, 0],
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#
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[ 1, 0, 0],
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[-1, 1, 0],
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[ 0, 1, 0],
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[ 1, 1, 0],
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#
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[-1,-1, 1],
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[ 0,-1, 1],
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[ 1,-1, 1],
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[-1, 0, 1],
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[ 0, 0, 1],
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[ 1, 0, 1],
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[-1, 1, 1],
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[ 0, 1, 1],
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[ 1, 1, 1],
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])
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}
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parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
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Produce geom files containing Euclidean distance to grain structural features:
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boundaries, triple lines, and quadruple points.
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""", version = scriptID)
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parser.add_option('-t','--type',
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dest = 'type',
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action = 'extend', metavar = '<string LIST>',
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help = 'feature type {%s} '%(', '.join(map(lambda x:'|'.join(x['alias']),features))) )
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parser.add_option('-n','--neighborhood',
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dest = 'neighborhood',
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choices = neighborhoods.keys(), metavar = 'string',
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help = 'type of neighborhood {%s} [neumann]'%(', '.join(neighborhoods.keys())))
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parser.add_option('-s', '--scale',
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dest = 'scale',
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type = 'float', metavar = 'float',
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help = 'voxel size [%default]')
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parser.set_defaults(type = [],
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neighborhood = 'neumann',
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scale = 1.0,
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)
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(options,filenames) = parser.parse_args()
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if len(options.type) == 0 or \
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not set(options.type).issubset(set(list(itertools.chain(*map(lambda x: x['alias'],features))))):
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parser.error('sleect feature type from (%s).'%(', '.join(map(lambda x:'|'.join(x['alias']),features))) )
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if 'biplane' in options.type and 'boundary' in options.type:
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parser.error("only one alias out 'biplane' and 'boundary' required")
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feature_list = []
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for i,feature in enumerate(features):
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for name in feature['alias']:
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for myType in options.type:
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if name.startswith(myType):
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feature_list.append(i) # remember selected features
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break
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# --- loop over input files -------------------------------------------------------------------------
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if filenames == []: filenames = [None]
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for name in filenames:
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try:
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table = damask.ASCIItable(name = name,
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buffered = False, labeled = False, readonly = True)
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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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table.head_read()
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info,extra_header = table.head_getGeom()
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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']))),
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'origin x y z: %s'%(' : '.join(map(str,info['origin']))),
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'homogenization: %i'%info['homogenization'],
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'microstructures: %i'%info['microstructures'],
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])
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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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# --- read data ------------------------------------------------------------------------------------
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microstructure = table.microstructure_read(info['grid']).reshape(info['grid'],order='F') # read microstructure
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table.close()
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neighborhood = neighborhoods[options.neighborhood]
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convoluted = np.empty([len(neighborhood)]+list(info['grid']+2),'i')
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structure = periodic_3Dpad(microstructure)
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for i,p in enumerate(neighborhood):
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stencil = np.zeros((3,3,3),'i')
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stencil[1,1,1] = -1
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stencil[p[0]+1,
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p[1]+1,
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p[2]+1] = 1
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convoluted[i,:,:,:] = ndimage.convolve(structure,stencil)
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convoluted = np.sort(convoluted,axis = 0)
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uniques = np.where(convoluted[0,1:-1,1:-1,1:-1] != 0, 1,0) # initialize unique value counter (exclude myself [= 0])
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for i in xrange(1,len(neighborhood)): # check remaining points in neighborhood
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uniques += np.where(np.logical_and(
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convoluted[i,1:-1,1:-1,1:-1] != convoluted[i-1,1:-1,1:-1,1:-1], # flip of ID difference detected?
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convoluted[i,1:-1,1:-1,1:-1] != 0), # not myself?
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1,0) # count flip
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for feature in feature_list:
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try:
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table = damask.ASCIItable(outname = features[feature]['alias'][0]+'_'+name if name else name,
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buffered = False, labeled = False)
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except: continue
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damask.util.croak(features[feature]['alias'][0])
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distance = np.where(uniques >= features[feature]['aliens'],0.0,1.0) # seed with 0.0 when enough unique neighbor IDs are present
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distance = ndimage.morphology.distance_transform_edt(distance)*[options.scale]*3
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info['microstructures'] = int(math.ceil(distance.max()))
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#--- write 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 {grid[0]}\tb {grid[1]}\tc {grid[2]}".format(grid=info['grid']),
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"size\tx {size[0]}\ty {size[1]}\tz {size[2]}".format(size=info['size']),
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"origin\tx {origin[0]}\ty {origin[1]}\tz {origin[2]}".format(origin=info['origin']),
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"homogenization\t{homog}".format(homog=info['homogenization']),
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"microstructures\t{microstructures}".format(microstructures=info['microstructures']),
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])
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table.labels_clear()
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table.head_write()
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# --- write microstructure information ------------------------------------------------------------
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formatwidth = int(math.floor(math.log10(distance.max())+1))
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table.data = distance.reshape((info['grid'][0],info['grid'][1]*info['grid'][2]),order='F').transpose()
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table.data_writeArray('%%%ii'%(formatwidth),delimiter=' ')
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#--- output finalization --------------------------------------------------------------------------
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table.close()
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@ -1,138 +0,0 @@
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#!/usr/bin/env python
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# -*- coding: UTF-8 no BOM -*-
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import os,itertools
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import numpy as np
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from optparse import OptionParser
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import damask
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scriptName = os.path.splitext(os.path.basename(__file__))[0]
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scriptID = ' '.join([scriptName,damask.version])
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#--------------------------------------------------------------------------------------------------
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# MAIN
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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 seed file by taking microstructure indices from given ASCIItable column.
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White and black-listing of microstructure indices is possible.
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Examples:
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--white 1,2,5 --index grainID isolates grainID entries of value 1, 2, and 5;
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--black 1 --index grainID takes all grainID entries except for value 1.
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""", version = scriptID)
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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.add_option('--boundingbox',
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dest = 'box',
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type = 'float', nargs = 6, metavar = ' '.join(['float']*6),
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help = 'min (x,y,z) and max (x,y,z) coordinates of bounding box [tight]')
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parser.add_option('-m',
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'--microstructure',
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dest = 'microstructure',
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type = 'string', metavar = 'string',
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help = 'label of microstructures [%default]')
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parser.add_option('--weight',
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dest = 'weight',
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type = 'string', metavar = 'string',
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help = 'label of weights [%default]')
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parser.add_option('-w',
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'--white',
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dest = 'whitelist',
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action = 'extend', metavar = '<int LIST>',
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help = 'whitelist of microstructure indices')
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parser.add_option('-b',
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'--black',
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dest = 'blacklist',
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action = 'extend', metavar = '<int LIST>',
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help = 'blacklist of microstructure indices')
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parser.set_defaults(pos = 'pos',
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microstructure = 'microstructure',
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weight = None,
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)
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(options,filenames) = parser.parse_args()
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if options.whitelist is not None: options.whitelist = map(int,options.whitelist)
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if options.blacklist is not None: options.blacklist = map(int,options.blacklist)
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# --- loop over input files -------------------------------------------------------------------------
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if filenames == []: filenames = [None]
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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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except: continue
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damask.util.report(scriptName,name)
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table.head_read() # read ASCII header info
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# ------------------------------------------ sanity checks ---------------------------------------
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missing_labels = table.data_readArray([options.pos,options.microstructure] +
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([options.weight] if options.weight else []))
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errors = []
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if len(missing_labels) > 0:
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errors.append('column{} {} not found'.format('s' if len(missing_labels) > 1 else '',
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', '.join(missing_labels)))
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input = {options.pos: 3,
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options.microstructure: 1,}
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if options.weight: input.update({options.weight: 1})
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for label, dim in input.iteritems():
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if table.label_dimension(label) != dim:
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errors.append('column {} has wrong dimension'.format(label))
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if errors != []:
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damask.util.croak(errors)
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table.close(dismiss = True) # close ASCII table file handles and delete output file
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continue
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# ------------------------------------------ process data ------------------------------------------
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# --- finding bounding box -------------------------------------------------------------------------
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boundingBox = np.array((np.amin(table.data[:,0:3],axis = 0),np.amax(table.data[:,0:3],axis = 0)))
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if options.box:
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boundingBox[0,:] = np.minimum(options.box[0:3],boundingBox[0,:])
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boundingBox[1,:] = np.maximum(options.box[3:6],boundingBox[1,:])
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# --- rescaling coordinates ------------------------------------------------------------------------
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table.data[:,0:3] -= boundingBox[0,:]
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table.data[:,0:3] /= boundingBox[1,:]-boundingBox[0,:]
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# --- filtering of grain voxels --------------------------------------------------------------------
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mask = np.logical_and(
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np.ones_like(table.data[:,3],bool) if options.whitelist is None \
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else np.in1d(table.data[:,3].ravel(), options.whitelist).reshape(table.data[:,3].shape),
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np.ones_like(table.data[:,3],bool) if options.blacklist is None \
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else np.invert(np.in1d(table.data[:,3].ravel(), options.blacklist).reshape(table.data[:,3].shape))
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)
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table.data = table.data[mask]
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# ------------------------------------------ assemble header ---------------------------------------
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table.info = [
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scriptID,
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'size {}'.format(' '.join(list(itertools.chain.from_iterable(zip(['x','y','z'],
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map(str,boundingBox[1,:]-boundingBox[0,:])))))),
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]
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table.labels_clear()
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table.labels_append(['1_pos','2_pos','3_pos','microstructure'] +
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['weight'] if options.weight else []) # implicitly switching label processing/writing on
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table.head_write()
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# ------------------------------------------ output result ---------------------------------------
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table.data_writeArray()
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table.close() # close ASCII tables
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