polished
This commit is contained in:
Martin Diehl
parent
07c9b8b8f0
commit
99da46fda8
2
PRIVATE
2
PRIVATE
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@ -1 +1 @@
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Subproject commit d326605a49b90dfdf3352f1a6a4ae8dd36507a13
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Subproject commit d596982319b5e8bbded6c14a5724df6c9de2a0fd
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@ -1,60 +1,72 @@
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#!/usr/bin/env python3
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# -*- coding: UTF-8 no BOM -*-
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import os
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import sys
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import numpy as np
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import damask
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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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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 option [geomfile(s)]', description = """
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Positions a geometric object within the (three-dimensional) canvas of a spectral geometry description.
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parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [geomfile(s)]', description = """
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Inserts a primitive geometric object at a given position.
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Depending on the sign of the dimension parameters, these objects can be boxes, cylinders, or ellipsoids.
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""", version = scriptID)
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parser.add_option('-c', '--center', dest='center',
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parser.add_option('-c', '--center',
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dest='center',
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type='float', nargs = 3, metavar=' '.join(['float']*3),
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help='a,b,c origin of primitive %default')
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parser.add_option('-d', '--dimension', dest='dimension',
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parser.add_option('-d', '--dimension',
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dest='dimension',
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type='float', nargs = 3, metavar=' '.join(['float']*3),
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help='a,b,c extension of hexahedral box; negative values are diameters')
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parser.add_option('-e', '--exponent', dest='exponent',
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help='a,b,c extension of hexahedral box')
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parser.add_option('-e', '--exponent',
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dest='exponent',
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type='float', nargs = 3, metavar=' '.join(['float']*3),
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help='i,j,k exponents for axes - 0 gives octahedron (|x|^(2^0) + |y|^(2^0) + |z|^(2^0) < 1), \
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1 gives a sphere (|x|^(2^1) + |y|^(2^1) + |z|^(2^1) < 1), \
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large values produce boxes, negative turns concave.')
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parser.add_option('-f', '--fill', dest='fill',
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type='float', metavar = 'float',
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help='grain index to fill primitive. "0" selects maximum microstructure index + 1 [%default]')
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parser.add_option('-q', '--quaternion', dest='quaternion',
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large values produce boxes, negative turn concave.')
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parser.add_option('-f', '--fill',
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dest='fill',
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type='float', metavar = 'int',
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help='microstructure index to fill primitive, defaults to max microstructure index + 1')
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parser.add_option('-q', '--quaternion',
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dest='quaternion',
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type='float', nargs = 4, metavar=' '.join(['float']*4),
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help = 'rotation of primitive as quaternion')
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parser.add_option('-a', '--angleaxis', dest='angleaxis', type=float,
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nargs = 4, metavar=' '.join(['float']*4),
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parser.add_option('-a', '--angleaxis',
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dest='angleaxis',
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type=float, nargs = 4, metavar=' '.join(['float']*4),
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help = 'axis and angle to rotate primitive')
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parser.add_option( '--degrees', dest='degrees',
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parser.add_option( '--degrees',
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dest='degrees',
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action='store_true',
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help = 'angle is given in degrees [%default]')
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parser.add_option( '--nonperiodic', dest='periodic',
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help = 'angle is given in degrees')
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parser.add_option( '--nonperiodic',
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dest='periodic',
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action='store_false',
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help = 'wrap around edges [%default]')
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parser.add_option( '--realspace', dest='realspace',
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help = 'wrap around edges')
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parser.add_option( '--realspace',
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dest='realspace',
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action='store_true',
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help = '-c and -d span [origin,origin+size] instead of [0,grid] coordinates')
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parser.add_option( '--invert', dest='inside',
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parser.add_option( '--invert',
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dest='inside',
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action='store_false',
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help = 'invert the volume filled by the primitive (inside/outside)')
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parser.set_defaults(center = (.0,.0,.0),
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fill = 0.0,
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degrees = False,
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exponent = (20,20,20), # box shape by default
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periodic = True,
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@ -65,7 +77,10 @@ parser.set_defaults(center = (.0,.0,.0),
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(options, filenames) = parser.parse_args()
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if options.dimension is None:
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parser.error('no dimension specified.')
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parser.error('no dimension specified.')
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if [options.angleaxis,options.quaternion].count(None) == 2:
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parser.error('more than one rotation specified.')
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if options.angleaxis is not None:
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rotation = damask.Rotation.fromAxisAngle(np.array(options.angleaxis),options.degrees,normalise=True)
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elif options.quaternion is not None:
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@ -73,22 +88,11 @@ elif options.quaternion is not None:
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else:
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rotation = damask.Rotation()
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options.center = np.array(options.center)
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options.center = np.array(options.center)
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options.dimension = np.array(options.dimension)
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# undo logarithmic sense of exponent and generate ellipsoids for negative dimensions (backward compatibility)
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options.exponent = np.where(np.array(options.dimension) > 0, np.power(2,options.exponent), 2)
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options.exponent = np.where(np.array(options.dimension) > 0, np.power(2,options.exponent), 2)
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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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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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# --- loop over input files -------------------------------------------------------------------------
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if filenames == []: filenames = [None]
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@ -100,9 +104,10 @@ for name in filenames:
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geom = damask.Geom.from_file(virt_file)
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else:
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geom = damask.Geom.from_file(name)
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microstructure = geom.microstructure
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damask.util.croak(geom)
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microstructure = geom.get_microstructure()
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options.fill = np.nanmax(microstructure)+1 if options.fill == 0 else options.fill
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fill = options.fill if options.fill is not None else np.nanmax(microstructure)+1
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origin = np.zeros(3)
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for i,line in enumerate(geom.comments):
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@ -176,20 +181,19 @@ for name in filenames:
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grid[2] * k : grid[2] * (k+1)])**options.exponent[2] <= 1.0)
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microstructure = np.where(inside,
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options.fill if options.inside else microstructure,
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microstructure if options.inside else options.fill)
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fill if options.inside else microstructure,
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microstructure if options.inside else fill)
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else: # nonperiodic, much lighter on resources
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microstructure = np.where(np.abs(X)**options.exponent[0] +
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np.abs(Y)**options.exponent[1] +
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np.abs(Z)**options.exponent[2] <= 1.0,
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options.fill if options.inside else microstructure,
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microstructure if options.inside else options.fill)
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fill if options.inside else microstructure,
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microstructure if options.inside else fill)
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geom.microstructure = microstructure
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damask.util.croak(geom.update(microstructure))
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geom.add_comment(scriptID + ' ' + ' '.join(sys.argv[1:]))
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damask.util.croak(geom)
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if name is None:
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sys.stdout.write(str(geom.show()))
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else:
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@ -1,160 +1,83 @@
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#!/usr/bin/env python3
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# -*- coding: UTF-8 no BOM -*-
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import os,sys,math
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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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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 option(s) [geomfile(s)]', description = """
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Changes the (three-dimensional) canvas of a spectral geometry description.
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parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [geomfile(s)]', description = """
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Increases or decreases the (three-dimensional) canvas.
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Grid can be given as absolute or relative values, e.g. 16 16 16 or 2x 0.5x 32.
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""", version = scriptID)
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parser.add_option('-g',
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'--grid',
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parser.add_option('-g','--grid',
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dest = 'grid',
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type = 'string', nargs = 3, metavar = ' '.join(['string']*3),
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help = 'a,b,c grid of hexahedral box. [auto]')
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parser.add_option('-o',
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'--offset',
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help = 'a,b,c grid of hexahedral box')
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parser.add_option('-o','--offset',
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dest = 'offset',
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type = 'int', nargs = 3, metavar = ' '.join(['int']*3),
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help = 'a,b,c offset from old to new origin of grid [%default]')
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parser.add_option('-f',
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'--fill',
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parser.add_option('-f','--fill',
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dest = 'fill',
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type = 'int', metavar = 'int',
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help = '(background) canvas grain index. "0" selects maximum microstructure index + 1 [%default]')
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type = 'float', metavar = 'int',
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help = 'background microstructure index, defaults to max microstructure index + 1')
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parser.set_defaults(grid = ('0','0','0'),
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offset = (0,0,0),
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)
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parser.set_defaults(offset = (0,0,0))
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(options, filenames) = parser.parse_args()
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datatype = 'i'
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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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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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if True:
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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.report_geom(info)
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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'],datatype).reshape(info['grid'],order='F') # read microstructure
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# --- do work ------------------------------------------------------------------------------------
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newInfo = {
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'grid': np.zeros(3,'i'),
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'origin': np.zeros(3,'d'),
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'microstructures': 0,
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}
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newInfo['grid'] = np.array([int(o*float(n.translate(None,'xX'))) if n[-1].lower() == 'x'\
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else int(n) for o,n in zip(info['grid'],options.grid)],'i')
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newInfo['grid'] = np.where(newInfo['grid'] > 0, newInfo['grid'],info['grid'])
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microstructure_cropped = np.zeros(newInfo['grid'],datatype)
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microstructure_cropped.fill(options.fill if options.fill is not None else np.nanmax(microstructure)+1)
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if True:
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xindex = np.arange(max(options.offset[0],0),min(options.offset[0]+newInfo['grid'][0],info['grid'][0]))
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yindex = np.arange(max(options.offset[1],0),min(options.offset[1]+newInfo['grid'][1],info['grid'][1]))
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zindex = np.arange(max(options.offset[2],0),min(options.offset[2]+newInfo['grid'][2],info['grid'][2]))
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translate_x = [i - options.offset[0] for i in xindex]
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translate_y = [i - options.offset[1] for i in yindex]
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translate_z = [i - options.offset[2] for i in zindex]
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if 0 in map(len,[xindex,yindex,zindex,translate_x,translate_y,translate_z]):
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damask.util.croak('invaldid combination of grid and offset.')
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table.close(dismiss = True)
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continue
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microstructure_cropped[min(translate_x):max(translate_x)+1,
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min(translate_y):max(translate_y)+1,
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min(translate_z):max(translate_z)+1] \
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= microstructure[min(xindex):max(xindex)+1,
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min(yindex):max(yindex)+1,
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min(zindex):max(zindex)+1]
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if name is None:
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virt_file = StringIO(''.join(sys.stdin.read()))
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geom = damask.Geom.from_file(virt_file)
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else:
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geom = damask.Geom.from_file(name)
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damask.util.croak(geom)
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microstructure = geom.get_microstructure()
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grid = geom.get_grid()
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if options.grid is not None:
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for i,g in enumerate(options.grid):
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grid[i] = int(round(grid[i]*float(g.lower().replace('x','')))) if g.lower().endswith('x') \
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else int(options.grid[i])
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newInfo['size'] = info['size']/info['grid']*newInfo['grid'] if np.all(info['grid'] > 0) else newInfo['grid']
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newInfo['origin'] = info['origin']+(info['size']/info['grid'] if np.all(info['grid'] > 0) \
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else newInfo['size']/newInfo['grid'])*options.offset
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newInfo['microstructures'] = len(np.unique(microstructure_cropped))
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new = np.full(grid,options.fill if options.fill is not None else np.nanmax(microstructure)+1,
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microstructure.dtype)
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for x in range(microstructure.shape[0]):
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X = x + options.offset[0]
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if not 0 <= X < new.shape[0]: continue
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for y in range(microstructure.shape[1]):
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Y = y + options.offset[1]
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if not 0 <= Y < new.shape[1]: continue
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for z in range(microstructure.shape[2]):
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Z = z + options.offset[2]
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if not 0 <= Z < new.shape[2]: continue
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new[X,Y,Z] = microstructure[x,y,z]
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# --- report ---------------------------------------------------------------------------------------
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damask.util.croak(geom.update(new,rescale=True))
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geom.add_comment(scriptID + ' ' + ' '.join(sys.argv[1:]))
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remarks = []
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errors = []
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if (any(newInfo['grid'] != info['grid'])):
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remarks.append('--> grid a b c: {}'.format(' x '.join(map(str,newInfo['grid']))))
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if (any(newInfo['size'] != info['size'])):
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remarks.append('--> size x y z: {}'.format(' x '.join(map(str,newInfo['size']))))
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if (any(newInfo['origin'] != info['origin'])):
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remarks.append('--> origin x y z: {}'.format(' : '.join(map(str,newInfo['origin']))))
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if ( newInfo['microstructures'] != info['microstructures']):
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remarks.append('--> microstructures: {}'.format(newInfo['microstructures']))
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if np.any(newInfo['grid'] < 1): errors.append('invalid new grid a b c.')
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if np.any(newInfo['size'] <= 0.0): errors.append('invalid new size x y z.')
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if remarks != []: damask.util.croak(remarks)
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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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# --- 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 {}\tb {}\tc {}".format(*newInfo['grid']),
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"size\tx {}\ty {}\tz {}".format(*newInfo['size']),
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"origin\tx {}\ty {}\tz {}".format(*newInfo['origin']),
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"homogenization\t{}".format(info['homogenization']),
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"microstructures\t{}".format(newInfo['microstructures']),
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])
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table.labels_clear()
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table.head_write()
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table.output_flush()
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# --- write microstructure information ------------------------------------------------------------
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format = '%{}i'.format(int(math.floor(math.log10(np.nanmax(microstructure_cropped))+1)))
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table.data = microstructure_cropped.reshape((newInfo['grid'][0],newInfo['grid'][1]*newInfo['grid'][2]),order='F').transpose()
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table.data_writeArray(format,delimiter=' ')
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# --- output finalization --------------------------------------------------------------------------
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table.close() # close ASCII table
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if name is None:
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sys.stdout.write(str(geom.show()))
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else:
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geom.to_file(name)
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@ -49,15 +49,15 @@ for name in filenames:
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geom = damask.Geom.from_file(virt_file)
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else:
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geom = damask.Geom.from_file(name)
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damask.util.croak(geom)
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microstructure = geom.get_microstructure()
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microstructure = ndimage.filters.generic_filter(microstructure,mostFrequent,
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size=(options.stencil,)*3).astype(microstructure.dtype)
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geom.set_microstructure(microstructure)
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damask.util.croak(geom.update(microstructure))
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geom.add_comment(scriptID + ' ' + ' '.join(sys.argv[1:]))
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damask.util.croak(geom)
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if name is None:
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sys.stdout.write(str(geom.show()))
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else:
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@ -1,21 +1,28 @@
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#!/usr/bin/env python3
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# -*- coding: UTF-8 no BOM -*-
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import os,sys,math
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import numpy as np
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import os
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||||
import sys
|
||||
from optparse import OptionParser
|
||||
|
||||
import numpy as np
|
||||
from scipy import ndimage
|
||||
|
||||
import damask
|
||||
|
||||
scriptName = os.path.splitext(os.path.basename(__file__))[0]
|
||||
scriptID = ' '.join([scriptName,damask.version])
|
||||
|
||||
|
||||
getInterfaceEnergy = lambda A,B: np.float32((A*B != 0)*(A != B)*1.0) # 1.0 if A & B are distinct & nonzero, 0.0 otherwise
|
||||
struc = ndimage.generate_binary_structure(3,1) # 3D von Neumann neighborhood
|
||||
|
||||
|
||||
#--------------------------------------------------------------------------------------------------
|
||||
# MAIN
|
||||
#--------------------------------------------------------------------------------------------------
|
||||
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog [option(s)] [geomfile(s)]', description = """
|
||||
Smoothens out interface roughness by simulated curvature flow.
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog option(s) [geomfile(s)]', description = """
|
||||
Smoothen interface roughness by simulated curvature flow.
|
||||
This is achieved by the diffusion of each initially sharply bounded grain volume within the periodic domain
|
||||
up to a given distance 'd' voxels.
|
||||
The final geometry is assembled by selecting at each voxel that grain index for which the concentration remains largest.
|
||||
|
|
@ -33,55 +40,33 @@ parser.add_option('-N', '--iterations',
|
|||
parser.add_option('-i', '--immutable',
|
||||
action = 'extend', dest = 'immutable', metavar = '<int LIST>',
|
||||
help = 'list of immutable microstructure indices')
|
||||
parser.add_option('-r', '--renumber',
|
||||
dest = 'renumber', action='store_true',
|
||||
help = 'output consecutive microstructure indices')
|
||||
parser.add_option('--ndimage',
|
||||
dest = 'ndimage', action='store_true',
|
||||
help = 'use ndimage.gaussian_filter in lieu of explicit FFT')
|
||||
|
||||
parser.set_defaults(d = 1,
|
||||
N = 1,
|
||||
immutable = [],
|
||||
renumber = False,
|
||||
ndimage = False,
|
||||
immutable = [],
|
||||
ndimage = False,
|
||||
)
|
||||
|
||||
(options, filenames) = parser.parse_args()
|
||||
|
||||
options.immutable = list(map(int,options.immutable))
|
||||
|
||||
getInterfaceEnergy = lambda A,B: np.float32((A*B != 0)*(A != B)*1.0) # 1.0 if A & B are distinct & nonzero, 0.0 otherwise
|
||||
struc = ndimage.generate_binary_structure(3,1) # 3D von Neumann neighborhood
|
||||
|
||||
# --- loop over input files -----------------------------------------------------------------------
|
||||
|
||||
if filenames == []: filenames = [None]
|
||||
|
||||
for name in filenames:
|
||||
try: table = damask.ASCIItable(name = name,
|
||||
buffered = False,
|
||||
labeled = False)
|
||||
except: continue
|
||||
damask.util.report(scriptName,name)
|
||||
|
||||
# --- interpret header ----------------------------------------------------------------------------
|
||||
|
||||
table.head_read()
|
||||
info,extra_header = table.head_getGeom()
|
||||
damask.util.report_geom(info)
|
||||
|
||||
errors = []
|
||||
if np.any(info['grid'] < 1): errors.append('invalid grid a b c.')
|
||||
if np.any(info['size'] <= 0.0): errors.append('invalid size x y z.')
|
||||
if errors != []:
|
||||
damask.util.croak(errors)
|
||||
table.close(dismiss = True)
|
||||
continue
|
||||
|
||||
# --- read data -----------------------------------------------------------------------------------
|
||||
microstructure = np.tile(table.microstructure_read(info['grid']).reshape(info['grid'],order='F'),
|
||||
np.where(info['grid'] == 1, 2,1)) # make one copy along dimensions with grid == 1
|
||||
|
||||
if name is None:
|
||||
virt_file = StringIO(''.join(sys.stdin.read()))
|
||||
geom = damask.Geom.from_file(virt_file)
|
||||
else:
|
||||
geom = damask.Geom.from_file(name)
|
||||
damask.util.croak(geom)
|
||||
|
||||
grid_original = geom.get_grid()
|
||||
microstructure = np.tile(geom.get_microstructure(),np.where(grid_original == 1, 2,1)) # make one copy along dimensions with grid == 1
|
||||
grid = np.array(microstructure.shape)
|
||||
|
||||
# --- initialize support data ---------------------------------------------------------------------
|
||||
|
|
@ -94,7 +79,7 @@ for name in filenames:
|
|||
|
||||
# Calculates gaussian weights for simulating 3d diffusion
|
||||
gauss = np.exp(-(X*X + Y*Y + Z*Z)/(2.0*options.d*options.d),dtype=np.float32) \
|
||||
/np.power(2.0*np.pi*options.d*options.d,(3.0 - np.count_nonzero(info['grid'] == 1))/2.,dtype=np.float32)
|
||||
/np.power(2.0*np.pi*options.d*options.d,(3.0 - np.count_nonzero(grid_original == 1))/2.,dtype=np.float32)
|
||||
|
||||
gauss[:,:,:grid[2]//2:-1] = gauss[:,:,1:(grid[2]+1)//2] # trying to cope with uneven (odd) grid size
|
||||
gauss[:,:grid[1]//2:-1,:] = gauss[:,1:(grid[1]+1)//2,:]
|
||||
|
|
@ -156,7 +141,7 @@ for name in filenames:
|
|||
# transform voxels close to interface region
|
||||
index = ndimage.morphology.distance_transform_edt(periodic_diffusedEnergy >= 0.95*np.amax(periodic_diffusedEnergy),
|
||||
return_distances = False,
|
||||
return_indices = True) # want index of closest bulk grain
|
||||
return_indices = True) # want index of closest bulk grain
|
||||
|
||||
periodic_microstructure = np.tile(microstructure,(3,3,3))[grid[0]//2:-grid[0]//2,
|
||||
grid[1]//2:-grid[1]//2,
|
||||
|
|
@ -184,49 +169,10 @@ for name in filenames:
|
|||
# undo any changes involving immutable microstructures
|
||||
microstructure = np.where(immutable, microstructure_original,microstructure)
|
||||
|
||||
# --- renumber to sequence 1...Ngrains if requested -----------------------------------------------
|
||||
# http://stackoverflow.com/questions/10741346/np-frequency-counts-for-unique-values-in-an-array
|
||||
damask.util.croak(geom.update(microstructure[0:grid_original[0],0:grid_original[1],0:grid_original[2]]))
|
||||
geom.add_comment(scriptID + ' ' + ' '.join(sys.argv[1:]))
|
||||
|
||||
if options.renumber:
|
||||
newID = 0
|
||||
for microstructureID,count in enumerate(np.bincount(microstructure.flatten())):
|
||||
if count != 0:
|
||||
newID += 1
|
||||
microstructure = np.where(microstructure == microstructureID, newID, microstructure)
|
||||
|
||||
newInfo = {'microstructures': len(np.unique(microstructure)),}
|
||||
|
||||
# --- report --------------------------------------------------------------------------------------
|
||||
|
||||
remarks = []
|
||||
if newInfo['microstructures'] != info['microstructures']:
|
||||
remarks.append('--> microstructures: {}'.format(newInfo['microstructures']))
|
||||
if remarks != []: damask.util.croak(remarks)
|
||||
|
||||
# --- write header --------------------------------------------------------------------------------
|
||||
|
||||
table.labels_clear()
|
||||
table.info_clear()
|
||||
table.info_append(extra_header+[
|
||||
scriptID + ' ' + ' '.join(sys.argv[1:]),
|
||||
"grid\ta {grid[0]}\tb {grid[1]}\tc {grid[2]}".format(grid=info['grid']),
|
||||
"size\tx {size[0]}\ty {size[1]}\tz {size[2]}".format(size=info['size']),
|
||||
"origin\tx {origin[0]}\ty {origin[1]}\tz {origin[2]}".format(origin=info['origin']),
|
||||
"homogenization\t{homog}".format(homog=info['homogenization']),
|
||||
"microstructures\t{microstructures}".format(microstructures=newInfo['microstructures']),
|
||||
])
|
||||
table.head_write()
|
||||
|
||||
# --- write microstructure information ------------------------------------------------------------
|
||||
|
||||
formatwidth = int(math.floor(math.log10(np.nanmax(microstructure))+1))
|
||||
table.data = microstructure[::1 if info['grid'][0]>1 else 2,
|
||||
::1 if info['grid'][1]>1 else 2,
|
||||
::1 if info['grid'][2]>1 else 2,].\
|
||||
reshape((info['grid'][0],info['grid'][1]*info['grid'][2]),order='F').transpose()
|
||||
table.data_writeArray('%{}i'.format(formatwidth),delimiter = ' ')
|
||||
|
||||
# --- output finalization --------------------------------------------------------------------------
|
||||
|
||||
table.close()
|
||||
|
||||
if name is None:
|
||||
sys.stdout.write(str(geom.show()))
|
||||
else:
|
||||
geom.to_file(name)
|
||||
|
|
|
|||
|
|
@ -18,7 +18,7 @@ scriptID = ' '.join([scriptName,damask.version])
|
|||
# MAIN
|
||||
#--------------------------------------------------------------------------------------------------
|
||||
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [geomfile(s)]', description = """
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog [geomfile(s)]', description = """
|
||||
Renumber sorted microstructure indices to 1,...,N.
|
||||
|
||||
""", version=scriptID)
|
||||
|
|
@ -36,16 +36,16 @@ for name in filenames:
|
|||
geom = damask.Geom.from_file(virt_file)
|
||||
else:
|
||||
geom = damask.Geom.from_file(name)
|
||||
damask.util.croak(geom)
|
||||
microstructure = geom.get_microstructure()
|
||||
|
||||
renumbered = np.copy(microstructure)
|
||||
for i, oldID in enumerate(np.unique(microstructure)):
|
||||
renumbered = np.where(microstructure == oldID, i+1, renumbered)
|
||||
|
||||
geom.set_microstructure(renumbered)
|
||||
damask.util.croak(geom.update(renumbered))
|
||||
geom.add_comment(scriptID + ' ' + ' '.join(sys.argv[1:]))
|
||||
|
||||
damask.util.croak(geom)
|
||||
if name is None:
|
||||
sys.stdout.write(str(geom.show()))
|
||||
else:
|
||||
|
|
|
|||
|
|
@ -53,13 +53,13 @@ for name in filenames:
|
|||
if options.grid is not None:
|
||||
for i,g in enumerate(options.grid):
|
||||
scale[i] = scale[i]*float(g.lower().replace('x','')) if g.lower().endswith('x') \
|
||||
else float(options.grid[i])/scale[i]
|
||||
else float(options.grid[i])/scale[i]
|
||||
|
||||
size = geom.get_size()
|
||||
if options.size is not None:
|
||||
for i,s in enumerate(options.size):
|
||||
size[i] = size[i]*float(s.lower().replace('x','')) if s.lower().endswith('x') \
|
||||
else options.size[i]
|
||||
else options.size[i]
|
||||
|
||||
microstructure = ndimage.interpolation.zoom(microstructure, scale, output=microstructure.dtype,
|
||||
order=0, mode='nearest', prefilter=False)
|
||||
|
|
|
|||
|
|
@ -1,22 +1,25 @@
|
|||
#!/usr/bin/env python3
|
||||
# -*- coding: UTF-8 no BOM -*-
|
||||
|
||||
import os
|
||||
import sys
|
||||
import numpy as np
|
||||
from optparse import OptionParser
|
||||
from io import StringIO
|
||||
|
||||
import numpy as np
|
||||
|
||||
import damask
|
||||
|
||||
|
||||
scriptName = os.path.splitext(os.path.basename(__file__))[0]
|
||||
scriptID = ' '.join([scriptName,damask.version])
|
||||
|
||||
|
||||
#--------------------------------------------------------------------------------------------------
|
||||
# MAIN
|
||||
#--------------------------------------------------------------------------------------------------
|
||||
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
|
||||
translate microstructure indices (shift or substitute) and/or geometry origin.
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [geomfile(s)]', description = """
|
||||
Translate microstructure indices (shift or substitute) and/or geometry origin.
|
||||
|
||||
""", version=scriptID)
|
||||
|
||||
|
|
@ -27,7 +30,7 @@ parser.add_option('-o', '--origin',
|
|||
parser.add_option('-m', '--microstructure',
|
||||
dest = 'microstructure',
|
||||
type = 'int', metavar = 'int',
|
||||
help = 'offset from old to new microstructure indices')
|
||||
help = 'offset from old to new microstructure indices (after substitution)')
|
||||
parser.add_option('-s', '--substitute',
|
||||
dest = 'substitute',
|
||||
action = 'extend', metavar = '<string LIST>',
|
||||
|
|
@ -44,7 +47,6 @@ sub = {}
|
|||
for i in range(len(options.substitute)//2): # split substitution list into "from" -> "to"
|
||||
sub[int(options.substitute[i*2])] = int(options.substitute[i*2+1])
|
||||
|
||||
# --- loop over input files -------------------------------------------------------------------------
|
||||
|
||||
if filenames == []: filenames = [None]
|
||||
|
||||
|
|
@ -56,11 +58,13 @@ for name in filenames:
|
|||
geom = damask.Geom.from_file(virt_file)
|
||||
else:
|
||||
geom = damask.Geom.from_file(name)
|
||||
microstructure = geom.microstructure
|
||||
damask.util.croak(geom)
|
||||
microstructure = geom.get_microstructure()
|
||||
new = np.copy(microstructure)
|
||||
|
||||
for k, v in sub.items(): microstructure[geom.microstructure==k] = v # substitute microstructure indices
|
||||
|
||||
microstructure += options.microstructure # shift microstructure indices
|
||||
for k, v in sub.items(): new[microstructure==k] = v # substitute microstructure indices and shift
|
||||
|
||||
microstructure += options.microstructure # constant shift
|
||||
|
||||
for i,line in enumerate(geom.comments):
|
||||
if line.lower().strip().startswith('origin'):
|
||||
|
|
@ -68,10 +72,9 @@ for name in filenames:
|
|||
origin += np.array(origin)
|
||||
geom.comments[i] = 'origin x {} y {} z {}'.format(*origin)
|
||||
|
||||
geom.microstructure = microstructure
|
||||
damask.util.croak(geom.update(microstructure))
|
||||
geom.add_comment(scriptID + ' ' + ' '.join(sys.argv[1:]))
|
||||
|
||||
damask.util.croak(geom)
|
||||
|
||||
if name is None:
|
||||
sys.stdout.write(str(geom.show()))
|
||||
else:
|
||||
|
|
|
|||
|
|
@ -1,17 +1,20 @@
|
|||
#!/usr/bin/env python3
|
||||
# -*- coding: UTF-8 no BOM -*-
|
||||
|
||||
import os
|
||||
import sys
|
||||
import numpy as np
|
||||
from scipy import ndimage
|
||||
from optparse import OptionParser
|
||||
from io import StringIO
|
||||
from optparse import OptionParser
|
||||
|
||||
from scipy import ndimage
|
||||
import numpy as np
|
||||
|
||||
import damask
|
||||
|
||||
|
||||
scriptName = os.path.splitext(os.path.basename(__file__))[0]
|
||||
scriptID = ' '.join([scriptName,damask.version])
|
||||
|
||||
|
||||
def taintedNeighborhood(stencil,trigger=[],size=1):
|
||||
|
||||
me = stencil[stencil.shape[0]//2]
|
||||
|
|
@ -23,11 +26,12 @@ def taintedNeighborhood(stencil,trigger=[],size=1):
|
|||
trigger = list(trigger)
|
||||
return np.any(np.in1d(stencil,np.array(trigger)))
|
||||
|
||||
|
||||
#--------------------------------------------------------------------------------------------------
|
||||
# MAIN
|
||||
#--------------------------------------------------------------------------------------------------
|
||||
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [geomfile(s)]', description = """
|
||||
Offset microstructure index for points which see a microstructure different from themselves
|
||||
(or listed as triggers) within a given (cubic) vicinity, i.e. within the region close to a grain/phase boundary.
|
||||
|
||||
|
|
@ -40,10 +44,10 @@ parser.add_option('-v', '--vicinity',
|
|||
parser.add_option('-m', '--microstructureoffset',
|
||||
dest='offset',
|
||||
type = 'int', metavar = 'int',
|
||||
help = 'offset (positive or negative) for tagged microstructure indices. '+
|
||||
'"0" selects maximum microstructure index [%default]')
|
||||
help='offset (positive or negative) to tag microstructure indices, defaults to max microstructure index + 1')
|
||||
parser.add_option('-t', '--trigger',
|
||||
action = 'extend', dest = 'trigger', metavar = '<int LIST>',
|
||||
dest = 'trigger',
|
||||
action = 'extend', metavar = '<int LIST>',
|
||||
help = 'list of microstructure indices triggering a change')
|
||||
parser.add_option('-n', '--nonperiodic',
|
||||
dest = 'mode',
|
||||
|
|
@ -51,17 +55,15 @@ parser.add_option('-n', '--nonperiodic',
|
|||
help = 'assume geometry to be non-periodic')
|
||||
|
||||
parser.set_defaults(vicinity = 1,
|
||||
offset = 0,
|
||||
trigger = [],
|
||||
mode = 'wrap',
|
||||
)
|
||||
|
||||
(options, filenames) = parser.parse_args()
|
||||
|
||||
options.trigger = np.array(options.trigger, dtype=int)
|
||||
|
||||
|
||||
# --- loop over input files -------------------------------------------------------------------------
|
||||
|
||||
if filenames == []: filenames = [None]
|
||||
|
||||
for name in filenames:
|
||||
|
|
@ -72,21 +74,21 @@ for name in filenames:
|
|||
geom = damask.Geom.from_file(virt_file)
|
||||
else:
|
||||
geom = damask.Geom.from_file(name)
|
||||
microstructure = geom.microstructure
|
||||
damask.util.croak(geom)
|
||||
microstructure = geom.get_microstructure()
|
||||
|
||||
if options.offset == 0: options.offset = microstructure.max()
|
||||
offset = options.offset if options.offset is not None else np.nanmax(microstructure)
|
||||
|
||||
microstructure = np.where(ndimage.filters.generic_filter(microstructure,
|
||||
taintedNeighborhood,
|
||||
size=1+2*options.vicinity,mode=options.mode,
|
||||
extra_arguments=(),
|
||||
extra_keywords={"trigger":options.trigger,"size":1+2*options.vicinity}),
|
||||
microstructure + options.offset,microstructure)
|
||||
microstructure + offset,microstructure)
|
||||
|
||||
geom.microstructure = microstructure
|
||||
damask.util.croak(geom.update(microstructure))
|
||||
geom.add_comment(scriptID + ' ' + ' '.join(sys.argv[1:]))
|
||||
|
||||
damask.util.croak(geom)
|
||||
if name is None:
|
||||
sys.stdout.write(str(geom.show()))
|
||||
else:
|
||||
|
|
|
|||
Loading…
Reference in New Issue